notebooks/CBTTC_snv.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {
    "toc": true
   },
   "source": [
    "<h1>Table of Contents<span class=\"tocSkip\"></span></h1>\n",
    "<div class=\"toc\"><ul class=\"toc-item\"><li><span><a href=\"#Overlap-Strelka2-and-Mutect2-calls-and-filter-variant-(VAF->-0.03)-for-CBTTC\" data-toc-modified-id=\"Overlap-Strelka2-and-Mutect2-calls-and-filter-variant-(VAF->-0.03)-for-CBTTC-1\">Overlap Strelka2 and Mutect2 calls and filter variant (VAF &gt; 0.03) for CBTTC</a></span></li><li><span><a href=\"#Dependencies\" data-toc-modified-id=\"Dependencies-2\">Dependencies</a></span></li><li><span><a href=\"#Paths\" data-toc-modified-id=\"Paths-3\">Paths</a></span></li><li><span><a href=\"#Main\" data-toc-modified-id=\"Main-4\">Main</a></span><ul class=\"toc-item\"><li><span><a href=\"#Overlap-variants-with-chr:start_pos\" data-toc-modified-id=\"Overlap-variants-with-chr:start_pos-4.1\">Overlap variants with chr:start_pos</a></span></li><li><span><a href=\"#Add-sample_id-from-clinical_df\" data-toc-modified-id=\"Add-sample_id-from-clinical_df-4.2\">Add sample_id from clinical_df</a></span></li></ul></li></ul></div>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Overlap Strelka2 and Mutect2 calls and filter variant (VAF > 0.03) for CBTTC"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Dependencies"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Warning message:\n",
      "“package ‘ggplot2’ was built under R version 3.5.2”"
     ]
    }
   ],
   "source": [
    "library(maftools)\n",
    "library(ggplot2)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Paths"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "manifestpath <- \"/Users/anabbi/OneDrive - UHN/Documents/IPD2/Manifests/\"\n",
    "datapath <- \"/Users/anabbi/OneDrive - UHN/Documents/IPD2/Data/\"\n",
    "plotpath <- \"/Users/anabbi/OneDrive - UHN/Documents/IPD2/Plots/\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Main"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "-Reading\n",
      "-Validating\n",
      "--Removed 120 duplicated variants\n",
      "-Summarizing\n",
      "--Possible FLAGS among top ten genes:\n",
      "  MUC17\n",
      "  AHNAK\n",
      "  AHNAK2\n",
      "  MUC16\n",
      "-Processing clinical data\n",
      "--Missing clinical data\n",
      "-Finished in 23.0s elapsed (23.9s cpu) \n"
     ]
    }
   ],
   "source": [
    "strelka2_CBTTC <- read.maf(maf = paste0(datapath, \"MAF_mat/CBTTC_recoded_mafs_KB_strelka2.maf\"),\n",
    "                      useAll = TRUE, \n",
    "                      verbose = T,\n",
    "                      vc_nonSyn = c(\"Frame_Shift_Del\", \"Frame_Shift_Ins\", \n",
    "                                    \"Nonsense_Mutation\",\"Nonstop_Mutation\", \n",
    "                                    \"In_Frame_Del\",\"In_Frame_Ins\", \n",
    "                                    \"Missense_Mutation\"))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "-Reading\n",
      "-Validating\n",
      "-Silent variants: 29837 \n",
      "-Summarizing\n",
      "--Possible FLAGS among top ten genes:\n",
      "  AHNAK2\n",
      "  MUC17\n",
      "  AHNAK\n",
      "-Processing clinical data\n",
      "--Missing clinical data\n",
      "-Finished in 9.216s elapsed (9.317s cpu) \n"
     ]
    }
   ],
   "source": [
    "mutect2_CBTTC <- read.maf(maf =  paste0(datapath, \"MAF_mat/CBTTC_Mutect2_combined_kb.maf\"),\n",
    "                      useAll = TRUE, \n",
    "                      verbose = T,\n",
    "                      vc_nonSyn = c(\"Frame_Shift_Del\", \"Frame_Shift_Ins\", \n",
    "                                    \"Nonsense_Mutation\",\"Nonstop_Mutation\", \n",
    "                                    \"In_Frame_Del\",\"In_Frame_Ins\", \n",
    "                                    \"Missense_Mutation\"))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "strelka2 <- strelka2_CBTTC@data\n",
    "mutect2 <- mutect2_CBTTC@data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A data.table: 6 × 147</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>Hugo_Symbol</th><th scope=col>Entrez_Gene_Id</th><th scope=col>Center</th><th scope=col>NCBI_Build</th><th scope=col>Chromosome</th><th scope=col>Start_Position</th><th scope=col>End_Position</th><th scope=col>Strand</th><th scope=col>Variant_Classification</th><th scope=col>Variant_Type</th><th scope=col>⋯</th><th scope=col>oncogenic</th><th scope=col>LEVEL_1</th><th scope=col>LEVEL_2A</th><th scope=col>LEVEL_2B</th><th scope=col>LEVEL_3A</th><th scope=col>LEVEL_3B</th><th scope=col>LEVEL_4</th><th scope=col>LEVEL_R1</th><th scope=col>Highest_level</th><th scope=col>citations</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;fct&gt;</th><th scope=col>&lt;fct&gt;</th><th scope=col>⋯</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;lgl&gt;</th><th scope=col>&lt;lgl&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;lgl&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;lgl&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>ATPAF1</td><td> 64756</td><td>.</td><td>GRCh38</td><td>chr1</td><td> 46668153</td><td> 46668153</td><td>+</td><td>Missense_Mutation</td><td>SNP</td><td>⋯</td><td></td><td>NA</td><td>NA</td><td></td><td>NA</td><td></td><td></td><td>NA</td><td></td><td></td></tr>\n",
       "\t<tr><td>TCHH  </td><td>  7062</td><td>.</td><td>GRCh38</td><td>chr1</td><td>152108268</td><td>152108268</td><td>+</td><td>Missense_Mutation</td><td>SNP</td><td>⋯</td><td></td><td>NA</td><td>NA</td><td></td><td>NA</td><td></td><td></td><td>NA</td><td></td><td></td></tr>\n",
       "\t<tr><td>FLG2  </td><td>388698</td><td>.</td><td>GRCh38</td><td>chr1</td><td>152353047</td><td>152353047</td><td>+</td><td>Missense_Mutation</td><td>SNP</td><td>⋯</td><td></td><td>NA</td><td>NA</td><td></td><td>NA</td><td></td><td></td><td>NA</td><td></td><td></td></tr>\n",
       "\t<tr><td>OR2T34</td><td>127068</td><td>.</td><td>GRCh38</td><td>chr1</td><td>248574433</td><td>248574433</td><td>+</td><td>Missense_Mutation</td><td>SNP</td><td>⋯</td><td></td><td>NA</td><td>NA</td><td></td><td>NA</td><td></td><td></td><td>NA</td><td></td><td></td></tr>\n",
       "\t<tr><td>NRXN1 </td><td>  9378</td><td>.</td><td>GRCh38</td><td>chr2</td><td> 51027791</td><td> 51027791</td><td>+</td><td>Missense_Mutation</td><td>SNP</td><td>⋯</td><td></td><td>NA</td><td>NA</td><td></td><td>NA</td><td></td><td></td><td>NA</td><td></td><td></td></tr>\n",
       "\t<tr><td>SPEG  </td><td> 10290</td><td>.</td><td>GRCh38</td><td>chr2</td><td>219483374</td><td>219483374</td><td>+</td><td>Missense_Mutation</td><td>SNP</td><td>⋯</td><td></td><td>NA</td><td>NA</td><td></td><td>NA</td><td></td><td></td><td>NA</td><td></td><td></td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.table: 6 × 147\n",
       "\\begin{tabular}{r|lllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllll}\n",
       " Hugo\\_Symbol & Entrez\\_Gene\\_Id & Center & NCBI\\_Build & Chromosome & Start\\_Position & End\\_Position & Strand & Variant\\_Classification & Variant\\_Type & Reference\\_Allele & Tumor\\_Seq\\_Allele1 & Tumor\\_Seq\\_Allele2 & dbSNP\\_RS & dbSNP\\_Val\\_Status & Tumor\\_Sample\\_Barcode & Matched\\_Norm\\_Sample\\_Barcode & Match\\_Norm\\_Seq\\_Allele1 & Match\\_Norm\\_Seq\\_Allele2 & Tumor\\_Validation\\_Allele1 & Tumor\\_Validation\\_Allele2 & Match\\_Norm\\_Validation\\_Allele1 & Match\\_Norm\\_Validation\\_Allele2 & Verification\\_Status & Validation\\_Status & Mutation\\_Status & Sequencing\\_Phase & Sequence\\_Source & Validation\\_Method & Score & BAM\\_File & Sequencer & Tumor\\_Sample\\_UUID & Matched\\_Norm\\_Sample\\_UUID & HGVSc & HGVSp & HGVSp\\_Short & Transcript\\_ID & Exon\\_Number & t\\_depth & t\\_ref\\_count & t\\_alt\\_count & n\\_depth & n\\_ref\\_count & n\\_alt\\_count & all\\_effects & Allele & Gene & Feature & Feature\\_type & Consequence & cDNA\\_position & CDS\\_position & Protein\\_position & Amino\\_acids & Codons & Existing\\_variation & ALLELE\\_NUM & DISTANCE & STRAND\\_VEP & SYMBOL & SYMBOL\\_SOURCE & HGNC\\_ID & BIOTYPE & CANONICAL & CCDS & ENSP & SWISSPROT & TREMBL & UNIPARC & RefSeq & SIFT & PolyPhen & EXON & INTRON & DOMAINS & AF & AFR\\_AF & AMR\\_AF & ASN\\_AF & EAS\\_AF & EUR\\_AF & SAS\\_AF & AA\\_AF & EA\\_AF & CLIN\\_SIG & SOMATIC & PUBMED & MOTIF\\_NAME & MOTIF\\_POS & HIGH\\_INF\\_POS & MOTIF\\_SCORE\\_CHANGE & IMPACT & PICK & VARIANT\\_CLASS & TSL & HGVS\\_OFFSET & PHENO & MINIMISED & ExAC\\_AF & ExAC\\_AF\\_AFR & ExAC\\_AF\\_AMR & ExAC\\_AF\\_EAS & ExAC\\_AF\\_FIN & ExAC\\_AF\\_NFE & ExAC\\_AF\\_OTH & ExAC\\_AF\\_SAS & GENE\\_PHENO & FILTER & flanking\\_bps & variant\\_id & variant\\_qual & ExAC\\_AF\\_Adj & ExAC\\_AC\\_AN\\_Adj & ExAC\\_AC\\_AN & ExAC\\_AC\\_AN\\_AFR & ExAC\\_AC\\_AN\\_AMR & ExAC\\_AC\\_AN\\_EAS & ExAC\\_AC\\_AN\\_FIN & ExAC\\_AC\\_AN\\_NFE & ExAC\\_AC\\_AN\\_OTH & ExAC\\_AC\\_AN\\_SAS & ExAC\\_FILTER & gnomAD\\_AF & gnomAD\\_AFR\\_AF & gnomAD\\_AMR\\_AF & gnomAD\\_ASJ\\_AF & gnomAD\\_EAS\\_AF & gnomAD\\_FIN\\_AF & gnomAD\\_NFE\\_AF & gnomAD\\_OTH\\_AF & gnomAD\\_SAS\\_AF & filename & inbed & is-a-hotspot & is-a-3d-hotspot & mutation\\_effect & oncogenic & LEVEL\\_1 & LEVEL\\_2A & LEVEL\\_2B & LEVEL\\_3A & LEVEL\\_3B & LEVEL\\_4 & LEVEL\\_R1 & Highest\\_level & citations\\\\\n",
       " <chr> & <int> & <chr> & <chr> & <chr> & <int> & <int> & <chr> & <fct> & <fct> & <chr> & <chr> & <chr> & <chr> & <lgl> & <fct> & <chr> & <chr> & <chr> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <chr> & <chr> & <chr> & <chr> & <chr> & <int> & <chr> & <int> & <int> & <chr> & <int> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <int> & <lgl> & <int> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <dbl> & <dbl> & <dbl> & <lgl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <chr> & <chr> & <chr> & <lgl> & <lgl> & <lgl> & <lgl> & <chr> & <int> & <chr> & <int> & <int> & <chr> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <int> & <chr> & <chr> & <chr> & <chr> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <lgl> & <lgl> & <chr> & <lgl> & <chr> & <chr> & <lgl> & <chr> & <chr>\\\\\n",
       "\\hline\n",
       "\t ATPAF1 &  64756 & . & GRCh38 & chr1 &  46668153 &  46668153 & + & Missense\\_Mutation & SNP & T & T & G & novel        & NA & BS\\_78TQS4Y3 & BS\\_RX561Y2K & T & T & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & c.239A>C  & p.Glu80Ala   & p.E80A   & ENST00000576409 & 1/9   & 46 & 32 &  9 & 25 & 24 & 0 & ATPAF1,missense\\_variant,p.Glu80Ala,ENST00000576409,;ATPAF1,missense\\_variant,p.Glu80Ala,ENST00000371937,NM\\_022745.4;ATPAF1,missense\\_variant,p.Glu57Ala,ENST00000574428,;ATPAF1,missense\\_variant,p.Glu80Ala,ENST00000329231,NM\\_001042546.2;TEX38,upstream\\_gene\\_variant,,ENST00000334122,NM\\_001145474.3;TEX38,upstream\\_gene\\_variant,,ENST00000415500,NM\\_001300864.1;ATPAF1,upstream\\_gene\\_variant,,ENST00000526821,;ATPAF1,upstream\\_gene\\_variant,,ENST00000532925,NM\\_001243728.1;ATPAF1,upstream\\_gene\\_variant,,ENST00000542495,NM\\_001256418.1;TEX38,upstream\\_gene\\_variant,,ENST00000564071,;TEX38,upstream\\_gene\\_variant,,ENST00000564373,NM\\_001300863.1;ATPAF1,intron\\_variant,,ENST00000525633,;ATPAF1,missense\\_variant,p.Glu10Ala,ENST00000487193,;ATPAF1,upstream\\_gene\\_variant,,ENST00000460928,;ATPAF1,upstream\\_gene\\_variant,,ENST00000474020,;ATPAF1,upstream\\_gene\\_variant,,ENST00000529214,;,regulatory\\_region\\_variant,,ENSR00000006005,;NENFP1,upstream\\_gene\\_variant,,ENST00000419476,;                                                                                                                                                       & G & ENSG00000123472 & ENST00000576409 & Transcript & missense\\_variant & 302/4158   & 239/1056  & 80/351    & E/A & gAg/gCg &                          & 1 & NA & -1 & ATPAF1 & HGNC & HGNC:18803 & protein\\_coding & YES & CCDS541.2   & ENSP00000460964 &        & I3L448 & UPI000222BB4E &                & tolerated\\_low\\_confidence(0.85) & benign(0.001) & 1/9   &  & hmmpanther:PTHR13126                                                                                                                                                                                                          &    NA & NA & NA & NA &    NA &    NA & NA & NA & NA &  &     & NA & NA & NA & NA & NA & MODERATE &  1 & SNV &  1 & NA &     & NA & NA & NA & NA & NA & NA & NA & NA & NA &  1 & PASS & CTC & . & . & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA &        NA &     NA &      NA &     NA &     NA &      NA &      NA &      NA &        NA & 000a6d41-be14-43dc-bdac-763b891b0184.strelka.vep.maf & FOUND &  &  &  &  & NA & NA &  & NA &  &  & NA &  & \\\\\n",
       "\t TCHH   &   7062 & . & GRCh38 & chr1 & 152108268 & 152108268 & + & Missense\\_Mutation & SNP & G & G & T & rs530417912  & NA & BS\\_78TQS4Y3 & BS\\_RX561Y2K & G & G & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & c.4949C>A & p.Pro1650Gln & p.P1650Q & ENST00000614923 & 3/3   & 69 & 55 & 11 & 40 & 38 & 1 & TCHH,missense\\_variant,p.Pro1650Gln,ENST00000614923,NM\\_007113.3;TCHH,missense\\_variant,p.Pro1650Gln,ENST00000368804,;,regulatory\\_region\\_variant,,ENSR00000013721,;,regulatory\\_region\\_variant,,ENSR00000254425,;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   & T & ENSG00000159450 & ENST00000614923 & Transcript & missense\\_variant & 5044/6995  & 4949/5832 & 1650/1943 & P/Q & cCg/cAg & rs530417912,COSM4221222  & 1 & NA & -1 & TCHH   & HGNC & HGNC:11791 & protein\\_coding & YES & CCDS41396.1 & ENSP00000480484 & Q07283 &        & UPI0000458A5E & NM\\_007113.3    & tolerated\\_low\\_confidence(0.54) & benign(0)     & 3/3   &  & Low\\_complexity\\_(Seg):seg,mobidb-lite,hmmpanther:PTHR34855,hmmpanther:PTHR34855                                                                                                                                                & 6e-04 & NA & NA & NA & 0.002 & 0.001 & NA & NA & NA &  & 0,1 & NA & NA & NA & NA & NA & MODERATE &  1 & SNV &  5 & NA & 0,1 & NA & NA & NA & NA & NA & NA & NA & NA & NA &  1 & PASS & CGG & . & . & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & 1.355e-05 &     NA &      NA &     NA &     NA &      NA &      NA &      NA & 0.0001116 & 000a6d41-be14-43dc-bdac-763b891b0184.strelka.vep.maf & FOUND &  &  &  &  & NA & NA &  & NA &  &  & NA &  & \\\\\n",
       "\t FLG2   & 388698 & . & GRCh38 & chr1 & 152353047 & 152353047 & + & Missense\\_Mutation & SNP & G & G & C & rs1255250864 & NA & BS\\_78TQS4Y3 & BS\\_RX561Y2K & G & G & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & c.4739C>G & p.Thr1580Ser & p.T1580S & ENST00000388718 & 3/3   & 80 & 63 & 14 & 37 & 36 & 1 & FLG2,missense\\_variant,p.Thr1580Ser,ENST00000388718,NM\\_001014342.2;FLG-AS1,intron\\_variant,,ENST00000392688,;FLG-AS1,intron\\_variant,,ENST00000445097,;FLG-AS1,intron\\_variant,,ENST00000629331,;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   & C & ENSG00000143520 & ENST00000388718 & Transcript & missense\\_variant & 4812/9124  & 4739/7176 & 1580/2391 & T/S & aCt/aGt & rs1255250864,COSM1295098 & 1 & NA & -1 & FLG2   & HGNC & HGNC:33276 & protein\\_coding & YES & CCDS30861.1 & ENSP00000373370 & Q5D862 &        & UPI00004E1DE5 & NM\\_001014342.2 & tolerated(1)                   & benign(0)     & 3/3   &  & mobidb-lite,hmmpanther:PTHR22571,hmmpanther:PTHR22571:SF24                                                                                                                                                                    &    NA & NA & NA & NA &    NA &    NA & NA & NA & NA &  & 0,1 & NA & NA & NA & NA & NA & MODERATE & NA & SNV &  5 & NA & 0,1 & NA & NA & NA & NA & NA & NA & NA & NA & NA &  1 & PASS & AGT & . & . & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA &        NA &     NA &      NA &     NA &     NA &      NA &      NA &      NA &        NA & 000a6d41-be14-43dc-bdac-763b891b0184.strelka.vep.maf & FOUND &  &  &  &  & NA & NA &  & NA &  &  & NA &  & \\\\\n",
       "\t OR2T34 & 127068 & . & GRCh38 & chr1 & 248574433 & 248574433 & + & Missense\\_Mutation & SNP & G & G & A & rs139616012  & NA & BS\\_78TQS4Y3 & BS\\_RX561Y2K & G & G & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & c.325C>T  & p.His109Tyr  & p.H109Y  & ENST00000328782 & 1/1   & 67 & 58 &  9 & 41 & 40 & 0 & OR2T34,missense\\_variant,p.His109Tyr,ENST00000328782,NM\\_001001821.1;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             & A & ENSG00000183310 & ENST00000328782 & Transcript & missense\\_variant & 325/957    & 325/957   & 109/318   & H/Y & Cac/Tac & rs139616012,COSM425943   & 1 & NA & -1 & OR2T34 & HGNC & HGNC:31256 & protein\\_coding & YES & CCDS31120.1 & ENSP00000330904 & Q8NGX1 &        & UPI0000061ED4 & NM\\_001001821.1 & tolerated(1)                   & benign(0)     & 1/1   &  & Gene3D:1.20.1070.10,Pfam\\_domain:PF13853,Prints\\_domain:PR00237,PROSITE\\_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF4,SMART\\_domains:SM01381,Superfamily\\_domains:SSF81321,Transmembrane\\_helices:TMhelix,cd15421 &    NA & NA & NA & NA &    NA &    NA & NA & NA & NA &  & 0,1 & NA & NA & NA & NA & NA & MODERATE &  1 & SNV & NA & NA & 0,1 & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & PASS & TGG & . & . & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & 3.526e-02 & 0.1049 & 0.04922 & 0.0143 & 0.0946 & 0.01236 & 0.02201 & 0.03482 & 0.0318800 & 000a6d41-be14-43dc-bdac-763b891b0184.strelka.vep.maf & FOUND &  &  &  &  & NA & NA &  & NA &  &  & NA &  & \\\\\n",
       "\t NRXN1  &   9378 & . & GRCh38 & chr2 &  51027791 &  51027791 & + & Missense\\_Mutation & SNP & T & T & G & novel        & NA & BS\\_78TQS4Y3 & BS\\_RX561Y2K & T & T & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & c.483A>C  & p.Glu161Asp  & p.E161D  & ENST00000404971 & 2/24  & 64 & 54 &  8 & 35 & 35 & 0 & NRXN1,missense\\_variant,p.Glu161Asp,ENST00000406316,NM\\_004801.4;NRXN1,missense\\_variant,p.Glu161Asp,ENST00000625672,;NRXN1,missense\\_variant,p.Glu161Asp,ENST00000404971,NM\\_001135659.1;NRXN1,missense\\_variant,p.Glu161Asp,ENST00000401669,;NRXN1,missense\\_variant,p.Glu161Asp,ENST00000405472,;NRXN1,missense\\_variant,p.Glu161Asp,ENST00000405581,NM\\_001330079.1,NM\\_001330081.1;NRXN1,missense\\_variant,p.Glu161Asp,ENST00000630543,;NRXN1,missense\\_variant,p.Glu161Asp,ENST00000637511,;NRXN1,missense\\_variant,p.Glu161Asp,ENST00000628515,;NRXN1,missense\\_variant,p.Glu14Asp,ENST00000636066,;NRXN1,missense\\_variant,p.Glu161Asp,ENST00000626899,;NRXN1,missense\\_variant,p.Glu3Asp,ENST00000496792,;NRXN1,upstream\\_gene\\_variant,,ENST00000627198,;AC007402.1,upstream\\_gene\\_variant,,ENST00000440698,;NRXN1,downstream\\_gene\\_variant,,ENST00000635126,;NRXN1,downstream\\_gene\\_variant,,ENST00000635310,;NRXN1,downstream\\_gene\\_variant,,ENST00000636599,;NRXN1,downstream\\_gene\\_variant,,ENST00000637006,;NRXN1,upstream\\_gene\\_variant,,ENST00000637679,;NRXN1,downstream\\_gene\\_variant,,ENST00000638060,;,regulatory\\_region\\_variant,,ENSR00000290894,; & G & ENSG00000179915 & ENST00000404971 & Transcript & missense\\_variant & 1823/7578  & 483/4644  & 161/1547  & E/D & gaA/gaC &                          & 1 & NA & -1 & NRXN1  & HGNC & HGNC:8008  & protein\\_coding & YES & CCDS46282.1 & ENSP00000385142 & Q9ULB1 &        & UPI00015A218A & NM\\_001135659.1 & tolerated(1)                   & benign(0.014) & 2/24  &  & PROSITE\\_profiles:PS50025,cd00110,hmmpanther:PTHR44287,hmmpanther:PTHR44287:SF2,Pfam\\_domain:PF02210,Gene3D:2.60.120.200,SMART\\_domains:SM00282,Superfamily\\_domains:SSF49899                                                     &    NA & NA & NA & NA &    NA &    NA & NA & NA & NA &  &     & NA & NA & NA & NA & NA & MODERATE &  1 & SNV &  1 & NA &     & NA & NA & NA & NA & NA & NA & NA & NA & NA &  1 & PASS & GTT & . & . & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA &        NA &     NA &      NA &     NA &     NA &      NA &      NA &      NA &        NA & 000a6d41-be14-43dc-bdac-763b891b0184.strelka.vep.maf & FOUND &  &  &  &  & NA & NA &  & NA &  &  & NA &  & \\\\\n",
       "\t SPEG   &  10290 & . & GRCh38 & chr2 & 219483374 & 219483374 & + & Missense\\_Mutation & SNP & A & A & C & novel        & NA & BS\\_78TQS4Y3 & BS\\_RX561Y2K & A & A & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & c.5911A>C & p.Met1971Leu & p.M1971L & ENST00000312358 & 30/41 & 63 & 52 &  9 & 25 & 25 & 0 & SPEG,missense\\_variant,p.Met1971Leu,ENST00000312358,NM\\_005876.4;AC053503.1,intron\\_variant,,ENST00000429882,;SPEG,non\\_coding\\_transcript\\_exon\\_variant,,ENST00000485813,;,regulatory\\_region\\_variant,,ENSR00000130557,;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              & C & ENSG00000072195 & ENST00000312358 & Transcript & missense\\_variant & 6043/10782 & 5911/9804 & 1971/3267 & M/L & Atg/Ctg &                          & 1 & NA &  1 & SPEG   & HGNC & HGNC:16901 & protein\\_coding & YES & CCDS42824.1 & ENSP00000311684 & Q15772 &        & UPI000066D99E & NM\\_005876.4    & tolerated(0.18)                & benign(0)     & 30/41 &  & Gene3D:1.10.510.10,hmmpanther:PTHR45065,mobidb-lite                                                                                                                                                                           &    NA & NA & NA & NA &    NA &    NA & NA & NA & NA &  &     & NA & NA & NA & NA & NA & MODERATE & NA & SNV &  5 & NA &     & NA & NA & NA & NA & NA & NA & NA & NA & NA &  1 & PASS & CAT & . & . & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA &        NA &     NA &      NA &     NA &     NA &      NA &      NA &      NA &        NA & 000a6d41-be14-43dc-bdac-763b891b0184.strelka.vep.maf & FOUND &  &  &  &  & NA & NA &  & NA &  &  & NA &  & \\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.table: 6 × 147\n",
       "\n",
       "| Hugo_Symbol &lt;chr&gt; | Entrez_Gene_Id &lt;int&gt; | Center &lt;chr&gt; | NCBI_Build &lt;chr&gt; | Chromosome &lt;chr&gt; | Start_Position &lt;int&gt; | End_Position &lt;int&gt; | Strand &lt;chr&gt; | Variant_Classification &lt;fct&gt; | Variant_Type &lt;fct&gt; | ⋯ ⋯ | oncogenic &lt;chr&gt; | LEVEL_1 &lt;lgl&gt; | LEVEL_2A &lt;lgl&gt; | LEVEL_2B &lt;chr&gt; | LEVEL_3A &lt;lgl&gt; | LEVEL_3B &lt;chr&gt; | LEVEL_4 &lt;chr&gt; | LEVEL_R1 &lt;lgl&gt; | Highest_level &lt;chr&gt; | citations &lt;chr&gt; |\n",
       "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n",
       "| ATPAF1 |  64756 | . | GRCh38 | chr1 |  46668153 |  46668153 | + | Missense_Mutation | SNP | ⋯ | <!----> | NA | NA | <!----> | NA | <!----> | <!----> | NA | <!----> | <!----> |\n",
       "| TCHH   |   7062 | . | GRCh38 | chr1 | 152108268 | 152108268 | + | Missense_Mutation | SNP | ⋯ | <!----> | NA | NA | <!----> | NA | <!----> | <!----> | NA | <!----> | <!----> |\n",
       "| FLG2   | 388698 | . | GRCh38 | chr1 | 152353047 | 152353047 | + | Missense_Mutation | SNP | ⋯ | <!----> | NA | NA | <!----> | NA | <!----> | <!----> | NA | <!----> | <!----> |\n",
       "| OR2T34 | 127068 | . | GRCh38 | chr1 | 248574433 | 248574433 | + | Missense_Mutation | SNP | ⋯ | <!----> | NA | NA | <!----> | NA | <!----> | <!----> | NA | <!----> | <!----> |\n",
       "| NRXN1  |   9378 | . | GRCh38 | chr2 |  51027791 |  51027791 | + | Missense_Mutation | SNP | ⋯ | <!----> | NA | NA | <!----> | NA | <!----> | <!----> | NA | <!----> | <!----> |\n",
       "| SPEG   |  10290 | . | GRCh38 | chr2 | 219483374 | 219483374 | + | Missense_Mutation | SNP | ⋯ | <!----> | NA | NA | <!----> | NA | <!----> | <!----> | NA | <!----> | <!----> |\n",
       "\n"
      ],
      "text/plain": [
       "  Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position\n",
       "1 ATPAF1       64756         .      GRCh38     chr1        46668153     \n",
       "2 TCHH          7062         .      GRCh38     chr1       152108268     \n",
       "3 FLG2        388698         .      GRCh38     chr1       152353047     \n",
       "4 OR2T34      127068         .      GRCh38     chr1       248574433     \n",
       "5 NRXN1         9378         .      GRCh38     chr2        51027791     \n",
       "6 SPEG         10290         .      GRCh38     chr2       219483374     \n",
       "  End_Position Strand Variant_Classification Variant_Type ⋯ oncogenic LEVEL_1\n",
       "1  46668153    +      Missense_Mutation      SNP          ⋯           NA     \n",
       "2 152108268    +      Missense_Mutation      SNP          ⋯           NA     \n",
       "3 152353047    +      Missense_Mutation      SNP          ⋯           NA     \n",
       "4 248574433    +      Missense_Mutation      SNP          ⋯           NA     \n",
       "5  51027791    +      Missense_Mutation      SNP          ⋯           NA     \n",
       "6 219483374    +      Missense_Mutation      SNP          ⋯           NA     \n",
       "  LEVEL_2A LEVEL_2B LEVEL_3A LEVEL_3B LEVEL_4 LEVEL_R1 Highest_level citations\n",
       "1 NA                NA                        NA                              \n",
       "2 NA                NA                        NA                              \n",
       "3 NA                NA                        NA                              \n",
       "4 NA                NA                        NA                              \n",
       "5 NA                NA                        NA                              \n",
       "6 NA                NA                        NA                              "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "head(strelka2)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Find samples with both strelka2 and mutect2 calls"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "strelkaIDs <- as.character(strelka2$Tumor_Sample_Barcode[!duplicated(strelka2$Tumor_Sample_Barcode)])\n",
    "\n",
    "mutectIDs <- as.character(mutect2$Tumor_Sample_Barcode[!duplicated(mutect2$Tumor_Sample_Barcode)])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "944"
      ],
      "text/latex": [
       "944"
      ],
      "text/markdown": [
       "944"
      ],
      "text/plain": [
       "[1] 944"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "907"
      ],
      "text/latex": [
       "907"
      ],
      "text/markdown": [
       "907"
      ],
      "text/plain": [
       "[1] 907"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "length(strelkaIDs)\n",
    "length(mutectIDs)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "906"
      ],
      "text/latex": [
       "906"
      ],
      "text/markdown": [
       "906"
      ],
      "text/plain": [
       "[1] 906"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "length(strelkaIDs[strelkaIDs %in% mutectIDs])\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Overlap variants with chr:start_pos"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "strelka2$chrpos <- paste(strelka2$Chromosome, strelka2$Start_Position,sep = \":\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "mutect2$chrpos <- paste(mutect2$Chromosome, mutect2$Start_Position,sep = \":\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "#samples in strelka2\n",
    "strelkaIDs <- as.character(strelka2$Tumor_Sample_Barcode[!duplicated(strelka2$Tumor_Sample_Barcode)])\n",
    "#samples in mutect2\n",
    "mutectIDs <- as.character(mutect2$Tumor_Sample_Barcode[!duplicated(mutect2$Tumor_Sample_Barcode)])\n",
    "#overlapping samples\n",
    "overlapID <- strelkaIDs[strelkaIDs %in% mutectIDs]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "strelka2_sample <- strelka2[strelka2$Tumor_Sample_Barcode == overlapID[1],]\n",
    "mutect2_sample <- mutect2[mutect2$Tumor_Sample_Barcode == overlapID[1],]\n",
    "overlap_sample <- merge(strelka2_sample[, c(\"chrpos\", \"Hugo_Symbol\")], mutect2_sample, \n",
    "                        by = \"chrpos\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A data.table: 3 × 162</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>chrpos</th><th scope=col>Hugo_Symbol.x</th><th scope=col>Hugo_Symbol.y</th><th scope=col>Entrez_Gene_Id</th><th scope=col>Center</th><th scope=col>NCBI_Build</th><th scope=col>Chromosome</th><th scope=col>Start_Position</th><th scope=col>End_Position</th><th scope=col>Strand</th><th scope=col>⋯</th><th scope=col>oncogenic</th><th scope=col>LEVEL_1</th><th scope=col>LEVEL_2A</th><th scope=col>LEVEL_2B</th><th scope=col>LEVEL_3A</th><th scope=col>LEVEL_3B</th><th scope=col>LEVEL_4</th><th scope=col>LEVEL_R1</th><th scope=col>Highest_level</th><th scope=col>citations</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>⋯</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;lgl&gt;</th><th scope=col>&lt;lgl&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;lgl&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;lgl&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>chr13:106567726</td><td>ARGLU1</td><td>ARGLU1</td><td>55082</td><td>Mutect2</td><td>GRCh38</td><td>chr13</td><td>106567726</td><td>106567726</td><td>+</td><td>⋯</td><td></td><td>NA</td><td>NA</td><td></td><td>NA</td><td></td><td></td><td>NA</td><td></td><td></td></tr>\n",
       "\t<tr><td>chr2:219483374 </td><td>SPEG  </td><td>SPEG  </td><td>10290</td><td>Mutect2</td><td>GRCh38</td><td>chr2 </td><td>219483374</td><td>219483374</td><td>+</td><td>⋯</td><td></td><td>NA</td><td>NA</td><td></td><td>NA</td><td></td><td></td><td>NA</td><td></td><td></td></tr>\n",
       "\t<tr><td>chr3:51391480  </td><td>RBM15B</td><td>RBM15B</td><td>29890</td><td>Mutect2</td><td>GRCh38</td><td>chr3 </td><td> 51391480</td><td> 51391480</td><td>+</td><td>⋯</td><td></td><td>NA</td><td>NA</td><td></td><td>NA</td><td></td><td></td><td>NA</td><td></td><td></td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.table: 3 × 162\n",
       "\\begin{tabular}{r|llllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllll}\n",
       " chrpos & Hugo\\_Symbol.x & Hugo\\_Symbol.y & Entrez\\_Gene\\_Id & Center & NCBI\\_Build & Chromosome & Start\\_Position & End\\_Position & Strand & Variant\\_Classification & Variant\\_Type & Reference\\_Allele & Tumor\\_Seq\\_Allele1 & Tumor\\_Seq\\_Allele2 & dbSNP\\_RS & dbSNP\\_Val\\_Status & Tumor\\_Sample\\_Barcode & Matched\\_Norm\\_Sample\\_Barcode & Match\\_Norm\\_Seq\\_Allele1 & Match\\_Norm\\_Seq\\_Allele2 & Tumor\\_Validation\\_Allele1 & Tumor\\_Validation\\_Allele2 & Match\\_Norm\\_Validation\\_Allele1 & Match\\_Norm\\_Validation\\_Allele2 & Verification\\_Status & Validation\\_Status & Mutation\\_Status & Sequencing\\_Phase & Sequence\\_Source & Validation\\_Method & Score & BAM\\_File & Sequencer & Tumor\\_Sample\\_UUID & Matched\\_Norm\\_Sample\\_UUID & HGVSc & HGVSp & HGVSp\\_Short & Transcript\\_ID & Exon\\_Number & t\\_depth & t\\_ref\\_count & t\\_alt\\_count & n\\_depth & n\\_ref\\_count & n\\_alt\\_count & all\\_effects & Allele & Gene & Feature & Feature\\_type & Consequence & cDNA\\_position & CDS\\_position & Protein\\_position & Amino\\_acids & Codons & Existing\\_variation & ALLELE\\_NUM & DISTANCE & STRAND\\_VEP & SYMBOL & SYMBOL\\_SOURCE & HGNC\\_ID & BIOTYPE & CANONICAL & CCDS & ENSP & SWISSPROT & TREMBL & UNIPARC & RefSeq & SIFT & PolyPhen & EXON & INTRON & DOMAINS & AF & AFR\\_AF & AMR\\_AF & ASN\\_AF & EAS\\_AF & EUR\\_AF & SAS\\_AF & AA\\_AF & EA\\_AF & CLIN\\_SIG & SOMATIC & PUBMED & MOTIF\\_NAME & MOTIF\\_POS & HIGH\\_INF\\_POS & MOTIF\\_SCORE\\_CHANGE & IMPACT & PICK & VARIANT\\_CLASS & TSL & HGVS\\_OFFSET & PHENO & MINIMISED & ExAC\\_AF & ExAC\\_AF\\_AFR & ExAC\\_AF\\_AMR & ExAC\\_AF\\_EAS & ExAC\\_AF\\_FIN & ExAC\\_AF\\_NFE & ExAC\\_AF\\_OTH & ExAC\\_AF\\_SAS & GENE\\_PHENO & FILTER & flanking\\_bps & variant\\_id & variant\\_qual & ExAC\\_AF\\_Adj & ExAC\\_AC\\_AN\\_Adj & ExAC\\_AC\\_AN & ExAC\\_AC\\_AN\\_AFR & ExAC\\_AC\\_AN\\_AMR & ExAC\\_AC\\_AN\\_EAS & ExAC\\_AC\\_AN\\_FIN & ExAC\\_AC\\_AN\\_NFE & ExAC\\_AC\\_AN\\_OTH & ExAC\\_AC\\_AN\\_SAS & ExAC\\_FILTER & gnomAD\\_AF & gnomAD\\_AFR\\_AF & gnomAD\\_AMR\\_AF & gnomAD\\_ASJ\\_AF & gnomAD\\_EAS\\_AF & gnomAD\\_FIN\\_AF & gnomAD\\_NFE\\_AF & gnomAD\\_OTH\\_AF & gnomAD\\_SAS\\_AF & ALT\\_F1R2 & ALT\\_F2R1 & FOXOG & REF\\_F1R2 & REF\\_F2R1 & TLOD & gnomAD\\_AF\\_POPMAX & gnomAD\\_AF\\_AFR & gnomAD\\_AF\\_AMR & gnomAD\\_AF\\_ASJ & gnomAD\\_AF\\_EAS & gnomAD\\_AF\\_FIN & gnomAD\\_AF\\_NFE & gnomAD\\_AF\\_OTH & gnomAD\\_AF\\_SAS & is-a-hotspot & is-a-3d-hotspot & mutation\\_effect & oncogenic & LEVEL\\_1 & LEVEL\\_2A & LEVEL\\_2B & LEVEL\\_3A & LEVEL\\_3B & LEVEL\\_4 & LEVEL\\_R1 & Highest\\_level & citations\\\\\n",
       " <chr> & <chr> & <chr> & <int> & <chr> & <chr> & <chr> & <int> & <int> & <chr> & <fct> & <fct> & <chr> & <chr> & <chr> & <chr> & <lgl> & <fct> & <chr> & <chr> & <chr> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <chr> & <chr> & <chr> & <chr> & <chr> & <int> & <int> & <int> & <int> & <int> & <int> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <int> & <int> & <int> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <dbl> & <dbl> & <dbl> & <lgl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <chr> & <chr> & <chr> & <lgl> & <lgl> & <lgl> & <lgl> & <chr> & <int> & <chr> & <int> & <int> & <chr> & <lgl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <int> & <chr> & <chr> & <chr> & <chr> & <dbl> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <chr> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <chr> & <chr> & <chr> & <chr> & <lgl> & <lgl> & <chr> & <lgl> & <chr> & <chr> & <lgl> & <chr> & <chr>\\\\\n",
       "\\hline\n",
       "\t chr13:106567726 & ARGLU1 & ARGLU1 & 55082 & Mutect2 & GRCh38 & chr13 & 106567726 & 106567726 & + & Missense\\_Mutation & SNP & A & A & C & novel & NA & BS\\_78TQS4Y3 & BS\\_RX561Y2K & A & A & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & c.194T>G  & p.Val65Gly   & p.V65G   & ENST00000400198 & 1/4   & 53 & 45 & 8 & 36 & 36 & 0 & ARGLU1,missense\\_variant,p.Val65Gly,ENST00000400198,NM\\_018011.3;ARGLU1,upstream\\_gene\\_variant,,ENST00000360629,;,regulatory\\_region\\_variant,,ENSR00000065521,;                                                                                                                                                                                                                                                                                  & C & ENSG00000134884 & ENST00000400198 & Transcript & missense\\_variant & 439/3390   & 194/822   & 65/273    & V/G & gTg/gGg &  & 1 & NA & -1 & ARGLU1 & HGNC & HGNC:25482 & protein\\_coding & YES & CCDS41906.1 & ENSP00000383059 & Q9NWB6 & A0A024RDW4 & UPI00000373ED & NM\\_018011.3 & tolerated(0.25)                & benign(0)     & 1/4   &  & Low\\_complexity\\_(Seg):seg,mobidb-lite,hmmpanther:PTHR31711:SF1,hmmpanther:PTHR31711                     & NA & NA & NA & NA & NA & NA & NA & NA & NA &  &  &  & NA & NA & NA & NA & MODERATE &  1 & SNV &  1 & NA &  & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & PASS & CAC & . & . & NA &  &  &  &  &  &  &  &  &  &      & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & 11.31 & NA & NA & NA & NA & NA & NA & NA & NA & NA &  &  &  &  & NA & NA &  & NA &  &  & NA &  & \\\\\n",
       "\t chr2:219483374  & SPEG   & SPEG   & 10290 & Mutect2 & GRCh38 & chr2  & 219483374 & 219483374 & + & Missense\\_Mutation & SNP & A & A & C & novel & NA & BS\\_78TQS4Y3 & BS\\_RX561Y2K & A & A & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & c.5911A>C & p.Met1971Leu & p.M1971L & ENST00000312358 & 30/41 & 57 & 49 & 8 & 25 & 25 & 0 & SPEG,missense\\_variant,p.Met1971Leu,ENST00000312358,NM\\_005876.4;AC053503.1,intron\\_variant,,ENST00000429882,;SPEG,non\\_coding\\_transcript\\_exon\\_variant,,ENST00000485813,;,regulatory\\_region\\_variant,,ENSR00000130557,;                                                                                                                                                                                                                           & C & ENSG00000072195 & ENST00000312358 & Transcript & missense\\_variant & 6043/10782 & 5911/9804 & 1971/3267 & M/L & Atg/Ctg &  & 1 & NA &  1 & SPEG   & HGNC & HGNC:16901 & protein\\_coding & YES & CCDS42824.1 & ENSP00000311684 & Q15772 &            & UPI000066D99E & NM\\_005876.4 & tolerated(0.18)                & benign(0)     & 30/41 &  & Gene3D:1.10.510.10,hmmpanther:PTHR45065,mobidb-lite                                                    & NA & NA & NA & NA & NA & NA & NA & NA & NA &  &  &  & NA & NA & NA & NA & MODERATE & NA & SNV &  5 & NA &  & NA & NA & NA & NA & NA & NA & NA & NA & NA &  1 & PASS & CAT & . & . & NA &  &  &  &  &  &  &  &  &  & PASS & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & 9.64  & NA & NA & NA & NA & NA & NA & NA & NA & NA &  &  &  &  & NA & NA &  & NA &  &  & NA &  & \\\\\n",
       "\t chr3:51391480   & RBM15B & RBM15B & 29890 & Mutect2 & GRCh38 & chr3  &  51391480 &  51391480 & + & Missense\\_Mutation & SNP & A & A & C & novel & NA & BS\\_78TQS4Y3 & BS\\_RX561Y2K & A & A & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & c.81A>C   & p.Glu27Asp   & p.E27D   & ENST00000563281 & 1/1   & 63 & 55 & 8 & 22 & 22 & 0 & RBM15B,missense\\_variant,p.Glu27Asp,ENST00000563281,NM\\_013286.4;DCAF1,downstream\\_gene\\_variant,,ENST00000423656,NM\\_014703.2;DCAF1,downstream\\_gene\\_variant,,ENST00000504652,NM\\_001171904.1;MANF,downstream\\_gene\\_variant,,ENST00000528157,NM\\_006010.5;MANF,downstream\\_gene\\_variant,,ENST00000470900,;MANF,downstream\\_gene\\_variant,,ENST00000446668,;MANF,downstream\\_gene\\_variant,,ENST00000482262,;,regulatory\\_region\\_variant,,ENSR00000152421,; & C & ENSG00000259956 & ENST00000563281 & Transcript & missense\\_variant & 213/6641   & 81/2673   & 27/890    & E/D & gaA/gaC &  & 1 & NA &  1 & RBM15B & HGNC & HGNC:24303 & protein\\_coding & YES & CCDS33764.1 & ENSP00000454545 & Q8NDT2 &            & UPI0000160BDE & NM\\_013286.4 & tolerated\\_low\\_confidence(0.55) & benign(0.007) & 1/1   &  & Gene3D:3.30.70.330,hmmpanther:PTHR23189,hmmpanther:PTHR23189:SF40,mobidb-lite,Low\\_complexity\\_(Seg):seg & NA & NA & NA & NA & NA & NA & NA & NA & NA &  &  &  & NA & NA & NA & NA & MODERATE & NA & SNV & NA & NA &  & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & PASS & AAC & . & . & NA &  &  &  &  &  &  &  &  &  &      & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & 10.34 & NA & NA & NA & NA & NA & NA & NA & NA & NA &  &  &  &  & NA & NA &  & NA &  &  & NA &  & \\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.table: 3 × 162\n",
       "\n",
       "| chrpos &lt;chr&gt; | Hugo_Symbol.x &lt;chr&gt; | Hugo_Symbol.y &lt;chr&gt; | Entrez_Gene_Id &lt;int&gt; | Center &lt;chr&gt; | NCBI_Build &lt;chr&gt; | Chromosome &lt;chr&gt; | Start_Position &lt;int&gt; | End_Position &lt;int&gt; | Strand &lt;chr&gt; | ⋯ ⋯ | oncogenic &lt;chr&gt; | LEVEL_1 &lt;lgl&gt; | LEVEL_2A &lt;lgl&gt; | LEVEL_2B &lt;chr&gt; | LEVEL_3A &lt;lgl&gt; | LEVEL_3B &lt;chr&gt; | LEVEL_4 &lt;chr&gt; | LEVEL_R1 &lt;lgl&gt; | Highest_level &lt;chr&gt; | citations &lt;chr&gt; |\n",
       "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n",
       "| chr13:106567726 | ARGLU1 | ARGLU1 | 55082 | Mutect2 | GRCh38 | chr13 | 106567726 | 106567726 | + | ⋯ | <!----> | NA | NA | <!----> | NA | <!----> | <!----> | NA | <!----> | <!----> |\n",
       "| chr2:219483374  | SPEG   | SPEG   | 10290 | Mutect2 | GRCh38 | chr2  | 219483374 | 219483374 | + | ⋯ | <!----> | NA | NA | <!----> | NA | <!----> | <!----> | NA | <!----> | <!----> |\n",
       "| chr3:51391480   | RBM15B | RBM15B | 29890 | Mutect2 | GRCh38 | chr3  |  51391480 |  51391480 | + | ⋯ | <!----> | NA | NA | <!----> | NA | <!----> | <!----> | NA | <!----> | <!----> |\n",
       "\n"
      ],
      "text/plain": [
       "  chrpos          Hugo_Symbol.x Hugo_Symbol.y Entrez_Gene_Id Center  NCBI_Build\n",
       "1 chr13:106567726 ARGLU1        ARGLU1        55082          Mutect2 GRCh38    \n",
       "2 chr2:219483374  SPEG          SPEG          10290          Mutect2 GRCh38    \n",
       "3 chr3:51391480   RBM15B        RBM15B        29890          Mutect2 GRCh38    \n",
       "  Chromosome Start_Position End_Position Strand ⋯ oncogenic LEVEL_1 LEVEL_2A\n",
       "1 chr13      106567726      106567726    +      ⋯           NA      NA      \n",
       "2 chr2       219483374      219483374    +      ⋯           NA      NA      \n",
       "3 chr3        51391480       51391480    +      ⋯           NA      NA      \n",
       "  LEVEL_2B LEVEL_3A LEVEL_3B LEVEL_4 LEVEL_R1 Highest_level citations\n",
       "1          NA                        NA                              \n",
       "2          NA                        NA                              \n",
       "3          NA                        NA                              "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "overlap_sample"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of strelka2 calls for: BS_SKRY0BJ4\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 43\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of mutect2 calls for: BS_SKRY0BJ4\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 35\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of overlapping calls for: BS_SKRY0BJ4\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 1\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of strelka2 calls for: BS_SYWRCE3Z\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 30\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of mutect2 calls for: BS_SYWRCE3Z\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 10\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of overlapping calls for: BS_SYWRCE3Z\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 2\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of strelka2 calls for: BS_45913DTA\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 12\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of mutect2 calls for: BS_45913DTA\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 4\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of overlapping calls for: BS_45913DTA\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 3\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of strelka2 calls for: BS_AHT9PKVE\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 11\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of mutect2 calls for: BS_AHT9PKVE\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 11\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of overlapping calls for: BS_AHT9PKVE\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 2\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of strelka2 calls for: BS_2W200YK5\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 12\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of mutect2 calls for: BS_2W200YK5\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 7\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of overlapping calls for: BS_2W200YK5\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 6\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of strelka2 calls for: BS_F4D169Q7\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 50\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of mutect2 calls for: BS_F4D169Q7\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 20\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of overlapping calls for: BS_F4D169Q7\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 3\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of strelka2 calls for: BS_QD22MJJ5\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 28\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of mutect2 calls for: BS_QD22MJJ5\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 11\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of overlapping calls for: BS_QD22MJJ5\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 1\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of strelka2 calls for: BS_BX8AR74E\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 31\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of mutect2 calls for: BS_BX8AR74E\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 15\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of overlapping calls for: BS_BX8AR74E\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 14\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of strelka2 calls for: BS_9BGCH82S\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 8\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of mutect2 calls for: BS_9BGCH82S\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 18\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of overlapping calls for: BS_9BGCH82S\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 2\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of strelka2 calls for: BS_2VSN5YC5\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 42\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of mutect2 calls for: BS_2VSN5YC5\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 17\n"
     ]
    },
    {
     "name": "stderr",
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     "output_type": "stream",
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     "output_type": "stream",
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     "output_type": "stream",
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     "output_type": "stream",
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     "output_type": "stream",
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     "output_type": "stream",
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     "output_type": "stream",
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     "output_type": "stream",
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     "output_type": "stream",
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     "output_type": "stream",
     "text": [
      "[1] 23\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of overlapping calls for: BS_NG0CR0EP\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 7\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of strelka2 calls for: BS_WH8KWW5J\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 118\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of mutect2 calls for: BS_WH8KWW5J\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 71\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of overlapping calls for: BS_WH8KWW5J\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 61\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of strelka2 calls for: BS_80X7AVCP\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 32\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of mutect2 calls for: BS_80X7AVCP\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 25\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of overlapping calls for: BS_80X7AVCP\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 8\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of strelka2 calls for: BS_PV130A29\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 7\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of mutect2 calls for: BS_PV130A29\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 3\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of overlapping calls for: BS_PV130A29\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 1\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of strelka2 calls for: BS_JE1DF581\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 25\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of mutect2 calls for: BS_JE1DF581\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 17\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of overlapping calls for: BS_JE1DF581\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 17\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of strelka2 calls for: BS_N9BF56FP\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 41\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of mutect2 calls for: BS_N9BF56FP\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 55\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of overlapping calls for: BS_N9BF56FP\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 32\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of strelka2 calls for: BS_39Q80NT3\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 12\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of mutect2 calls for: BS_39Q80NT3\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 8\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of overlapping calls for: BS_39Q80NT3\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 7\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of strelka2 calls for: BS_ZAH4FHV2\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 49\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of mutect2 calls for: BS_ZAH4FHV2\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 21\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "number of overlapping calls for: BS_ZAH4FHV2\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] 12\n"
     ]
    }
   ],
   "source": [
    "for(id in overlapID[2:length(overlapID)]){\n",
    "    strelka2_sample <- strelka2[strelka2$Tumor_Sample_Barcode == id,]\n",
    "    mutect2_sample <- mutect2[mutect2$Tumor_Sample_Barcode == id,]\n",
    "    message(\"number of strelka2 calls for: \", id)\n",
    "    print(nrow(strelka2_sample))\n",
    "    message(\"number of mutect2 calls for: \", id)\n",
    "    print(nrow(mutect2_sample))\n",
    "    overlap_sample1 <- merge(strelka2_sample[, c(\"chrpos\", \"Hugo_Symbol\")], \n",
    "                            mutect2_sample, \n",
    "                            by = \"chrpos\")\n",
    "    overlap_sample <- rbind(overlap_sample,\n",
    "                           overlap_sample1)\n",
    "    message(\"number of overlapping calls for: \", id)\n",
    "    print(nrow(overlap_sample1))\n",
    "    \n",
    "}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "842"
      ],
      "text/latex": [
       "842"
      ],
      "text/markdown": [
       "842"
      ],
      "text/plain": [
       "[1] 842"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "length(as.character(overlap_sample$Tumor_Sample_Barcode[!duplicated(overlap_sample$Tumor_Sample_Barcode)]))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Are there any samples with no overlap?"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "strelka2$Tumor_Sample_Barcode <- as.character(strelka2$Tumor_Sample_Barcode)\n",
    "mutect2$Tumor_Sample_Barcode <- as.character(mutect2$Tumor_Sample_Barcode)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1] \"BS_CFEWVDG1\"\n",
      "[1] \"BS_HM5N78GV\"\n",
      "[1] \"BS_BVD7PWP5\"\n",
      "[1] \"BS_GCQEB05M\"\n",
      "[1] \"BS_XPSD2NRJ\"\n",
      "[1] \"BS_R1RMKH1B\"\n",
      "[1] \"BS_0XR7GYAV\"\n",
      "[1] \"BS_XKE77TR4\"\n",
      "[1] \"BS_T8C13KNH\"\n",
      "[1] \"BS_AXM96K20\"\n",
      "[1] \"BS_WD7AQV83\"\n",
      "[1] \"BS_N5VYY66W\"\n",
      "[1] \"BS_R94EDP5H\"\n",
      "[1] \"BS_8BM1WTGR\"\n",
      "[1] \"BS_CWQ35N2K\"\n",
      "[1] \"BS_9W6FK6X4\"\n",
      "[1] \"BS_17FVWMNV\"\n",
      "[1] \"BS_62XRDTM6\"\n",
      "[1] \"BS_WSFB4SA2\"\n",
      "[1] \"BS_GDPZN3SD\"\n",
      "[1] \"BS_PMSZKZP7\"\n",
      "[1] \"BS_MS87PMR7\"\n",
      "[1] \"BS_XVYRXN8J\"\n",
      "[1] \"BS_F7KYPE79\"\n",
      "[1] \"BS_HC4T1EEP\"\n",
      "[1] \"BS_5NAKYS1S\"\n",
      "[1] \"BS_CXN0498B\"\n",
      "[1] \"BS_PFXDWV9R\"\n",
      "[1] \"BS_MW6YMRBJ\"\n",
      "[1] \"BS_JJZPY3BG\"\n",
      "[1] \"BS_VHD4ARSG\"\n",
      "[1] \"BS_T97EP8H0\"\n",
      "[1] \"BS_4XPPZTGG\"\n",
      "[1] \"BS_YPCTK927\"\n",
      "[1] \"BS_8S2CZBA6\"\n",
      "[1] \"BS_6GTKRGNK\"\n",
      "[1] \"BS_JTBM5TSE\"\n",
      "[1] \"BS_CPZZR2R7\"\n",
      "[1] \"BS_BNFCXVYZ\"\n",
      "[1] \"BS_M1YHV93N\"\n",
      "[1] \"BS_EQE19CB0\"\n",
      "[1] \"BS_QSDKJM8T\"\n",
      "[1] \"BS_WRJNMEX2\"\n",
      "[1] \"BS_CP435MAC\"\n",
      "[1] \"BS_947CK40E\"\n",
      "[1] \"BS_XKXDH0YJ\"\n",
      "[1] \"BS_TPX7YY57\"\n",
      "[1] \"BS_PVZJCXS1\"\n",
      "[1] \"BS_BYJDRXMK\"\n",
      "[1] \"BS_BA0M71QZ\"\n",
      "[1] \"BS_C0YDDQKB\"\n",
      "[1] \"BS_SK949N33\"\n",
      "[1] \"BS_41SWNWAG\"\n",
      "[1] \"BS_Q807ENGY\"\n",
      "[1] \"BS_8JFMP1T1\"\n",
      "[1] \"BS_ZJT1REVB\"\n",
      "[1] \"BS_XDY9BYRK\"\n",
      "[1] \"BS_EKR4NSNW\"\n",
      "[1] \"BS_3C4YAMKJ\"\n",
      "[1] \"BS_KVV3G6NP\"\n",
      "[1] \"BS_NASADC3P\"\n",
      "[1] \"BS_D09VWF8H\"\n",
      "[1] \"BS_M9YZK3SP\"\n",
      "[1] \"BS_XHAQXDR0\"\n"
     ]
    }
   ],
   "source": [
    "for(id in overlapID[1:length(overlapID)]){\n",
    "    strelka2_sample <- strelka2[strelka2$Tumor_Sample_Barcode == id,]\n",
    "    mutect2_sample <- mutect2[mutect2$Tumor_Sample_Barcode == id,]\n",
    "    overlap_sample1 <- merge(strelka2_sample[, c(\"chrpos\", \"Hugo_Symbol\")], \n",
    "                            mutect2_sample, \n",
    "                            by = \"chrpos\")\n",
    "    if(nrow(overlap_sample1) == 0){\n",
    "        print(mutect2_sample$Tumor_Sample_Barcode[!duplicated(mutect2_sample$Tumor_Sample_Barcode)])}\n",
    "    \n",
    "}"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "64 cases had no mutations overlapping\n",
    "\n",
    "I ended up with 658 cases for which I had both rna and mutect2 results. using overlapped calls I will end up with 597 cases with both rna and mutation calls. See TMB_final_overlapped."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [],
   "source": [
    "overlap_sample$Hugo_Symbol.x <- NULL"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A data.table: 6 × 161</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>chrpos</th><th scope=col>Hugo_Symbol.y</th><th scope=col>Entrez_Gene_Id</th><th scope=col>Center</th><th scope=col>NCBI_Build</th><th scope=col>Chromosome</th><th scope=col>Start_Position</th><th scope=col>End_Position</th><th scope=col>Strand</th><th scope=col>Variant_Classification</th><th scope=col>⋯</th><th scope=col>oncogenic</th><th scope=col>LEVEL_1</th><th scope=col>LEVEL_2A</th><th scope=col>LEVEL_2B</th><th scope=col>LEVEL_3A</th><th scope=col>LEVEL_3B</th><th scope=col>LEVEL_4</th><th scope=col>LEVEL_R1</th><th scope=col>Highest_level</th><th scope=col>citations</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;fct&gt;</th><th scope=col>⋯</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;lgl&gt;</th><th scope=col>&lt;lgl&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;lgl&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;lgl&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>chr13:106567726</td><td>ARGLU1 </td><td> 55082</td><td>Mutect2</td><td>GRCh38</td><td>chr13</td><td>106567726</td><td>106567726</td><td>+</td><td>Missense_Mutation</td><td>⋯</td><td></td><td>NA</td><td>NA</td><td></td><td>NA</td><td></td><td></td><td>NA</td><td></td><td></td></tr>\n",
       "\t<tr><td>chr2:219483374 </td><td>SPEG   </td><td> 10290</td><td>Mutect2</td><td>GRCh38</td><td>chr2 </td><td>219483374</td><td>219483374</td><td>+</td><td>Missense_Mutation</td><td>⋯</td><td></td><td>NA</td><td>NA</td><td></td><td>NA</td><td></td><td></td><td>NA</td><td></td><td></td></tr>\n",
       "\t<tr><td>chr3:51391480  </td><td>RBM15B </td><td> 29890</td><td>Mutect2</td><td>GRCh38</td><td>chr3 </td><td> 51391480</td><td> 51391480</td><td>+</td><td>Missense_Mutation</td><td>⋯</td><td></td><td>NA</td><td>NA</td><td></td><td>NA</td><td></td><td></td><td>NA</td><td></td><td></td></tr>\n",
       "\t<tr><td>chr2:241803771 </td><td>GAL3ST2</td><td> 64090</td><td>Mutect2</td><td>GRCh38</td><td>chr2 </td><td>241803771</td><td>241803771</td><td>+</td><td>Missense_Mutation</td><td>⋯</td><td></td><td>NA</td><td>NA</td><td></td><td>NA</td><td></td><td></td><td>NA</td><td></td><td></td></tr>\n",
       "\t<tr><td>chr2:29073320  </td><td>C2orf71</td><td>388939</td><td>Mutect2</td><td>GRCh38</td><td>chr2 </td><td> 29073320</td><td> 29073320</td><td>+</td><td>Missense_Mutation</td><td>⋯</td><td></td><td>NA</td><td>NA</td><td></td><td>NA</td><td></td><td></td><td>NA</td><td></td><td></td></tr>\n",
       "\t<tr><td>chr4:56976960  </td><td>NOA1   </td><td> 84273</td><td>Mutect2</td><td>GRCh38</td><td>chr4 </td><td> 56976960</td><td> 56976960</td><td>+</td><td>Nonsense_Mutation</td><td>⋯</td><td></td><td>NA</td><td>NA</td><td></td><td>NA</td><td></td><td></td><td>NA</td><td></td><td></td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.table: 6 × 161\n",
       "\\begin{tabular}{r|lllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllllll}\n",
       " chrpos & Hugo\\_Symbol.y & Entrez\\_Gene\\_Id & Center & NCBI\\_Build & Chromosome & Start\\_Position & End\\_Position & Strand & Variant\\_Classification & Variant\\_Type & Reference\\_Allele & Tumor\\_Seq\\_Allele1 & Tumor\\_Seq\\_Allele2 & dbSNP\\_RS & dbSNP\\_Val\\_Status & Tumor\\_Sample\\_Barcode & Matched\\_Norm\\_Sample\\_Barcode & Match\\_Norm\\_Seq\\_Allele1 & Match\\_Norm\\_Seq\\_Allele2 & Tumor\\_Validation\\_Allele1 & Tumor\\_Validation\\_Allele2 & Match\\_Norm\\_Validation\\_Allele1 & Match\\_Norm\\_Validation\\_Allele2 & Verification\\_Status & Validation\\_Status & Mutation\\_Status & Sequencing\\_Phase & Sequence\\_Source & Validation\\_Method & Score & BAM\\_File & Sequencer & Tumor\\_Sample\\_UUID & Matched\\_Norm\\_Sample\\_UUID & HGVSc & HGVSp & HGVSp\\_Short & Transcript\\_ID & Exon\\_Number & t\\_depth & t\\_ref\\_count & t\\_alt\\_count & n\\_depth & n\\_ref\\_count & n\\_alt\\_count & all\\_effects & Allele & Gene & Feature & Feature\\_type & Consequence & cDNA\\_position & CDS\\_position & Protein\\_position & Amino\\_acids & Codons & Existing\\_variation & ALLELE\\_NUM & DISTANCE & STRAND\\_VEP & SYMBOL & SYMBOL\\_SOURCE & HGNC\\_ID & BIOTYPE & CANONICAL & CCDS & ENSP & SWISSPROT & TREMBL & UNIPARC & RefSeq & SIFT & PolyPhen & EXON & INTRON & DOMAINS & AF & AFR\\_AF & AMR\\_AF & ASN\\_AF & EAS\\_AF & EUR\\_AF & SAS\\_AF & AA\\_AF & EA\\_AF & CLIN\\_SIG & SOMATIC & PUBMED & MOTIF\\_NAME & MOTIF\\_POS & HIGH\\_INF\\_POS & MOTIF\\_SCORE\\_CHANGE & IMPACT & PICK & VARIANT\\_CLASS & TSL & HGVS\\_OFFSET & PHENO & MINIMISED & ExAC\\_AF & ExAC\\_AF\\_AFR & ExAC\\_AF\\_AMR & ExAC\\_AF\\_EAS & ExAC\\_AF\\_FIN & ExAC\\_AF\\_NFE & ExAC\\_AF\\_OTH & ExAC\\_AF\\_SAS & GENE\\_PHENO & FILTER & flanking\\_bps & variant\\_id & variant\\_qual & ExAC\\_AF\\_Adj & ExAC\\_AC\\_AN\\_Adj & ExAC\\_AC\\_AN & ExAC\\_AC\\_AN\\_AFR & ExAC\\_AC\\_AN\\_AMR & ExAC\\_AC\\_AN\\_EAS & ExAC\\_AC\\_AN\\_FIN & ExAC\\_AC\\_AN\\_NFE & ExAC\\_AC\\_AN\\_OTH & ExAC\\_AC\\_AN\\_SAS & ExAC\\_FILTER & gnomAD\\_AF & gnomAD\\_AFR\\_AF & gnomAD\\_AMR\\_AF & gnomAD\\_ASJ\\_AF & gnomAD\\_EAS\\_AF & gnomAD\\_FIN\\_AF & gnomAD\\_NFE\\_AF & gnomAD\\_OTH\\_AF & gnomAD\\_SAS\\_AF & ALT\\_F1R2 & ALT\\_F2R1 & FOXOG & REF\\_F1R2 & REF\\_F2R1 & TLOD & gnomAD\\_AF\\_POPMAX & gnomAD\\_AF\\_AFR & gnomAD\\_AF\\_AMR & gnomAD\\_AF\\_ASJ & gnomAD\\_AF\\_EAS & gnomAD\\_AF\\_FIN & gnomAD\\_AF\\_NFE & gnomAD\\_AF\\_OTH & gnomAD\\_AF\\_SAS & is-a-hotspot & is-a-3d-hotspot & mutation\\_effect & oncogenic & LEVEL\\_1 & LEVEL\\_2A & LEVEL\\_2B & LEVEL\\_3A & LEVEL\\_3B & LEVEL\\_4 & LEVEL\\_R1 & Highest\\_level & citations\\\\\n",
       " <chr> & <chr> & <int> & <chr> & <chr> & <chr> & <int> & <int> & <chr> & <fct> & <fct> & <chr> & <chr> & <chr> & <chr> & <lgl> & <fct> & <chr> & <chr> & <chr> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <chr> & <chr> & <chr> & <chr> & <chr> & <int> & <int> & <int> & <int> & <int> & <int> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <int> & <int> & <int> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <dbl> & <dbl> & <dbl> & <lgl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <chr> & <chr> & <chr> & <lgl> & <lgl> & <lgl> & <lgl> & <chr> & <int> & <chr> & <int> & <int> & <chr> & <lgl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <int> & <chr> & <chr> & <chr> & <chr> & <dbl> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <chr> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <lgl> & <chr> & <chr> & <chr> & <chr> & <lgl> & <lgl> & <chr> & <lgl> & <chr> & <chr> & <lgl> & <chr> & <chr>\\\\\n",
       "\\hline\n",
       "\t chr13:106567726 & ARGLU1  &  55082 & Mutect2 & GRCh38 & chr13 & 106567726 & 106567726 & + & Missense\\_Mutation & SNP & A & A & C & novel & NA & BS\\_78TQS4Y3 & BS\\_RX561Y2K & A & A & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & c.194T>G  & p.Val65Gly   & p.V65G   & ENST00000400198 & 1/4   &  53 & 45 &  8 & 36 & 36 & 0 & ARGLU1,missense\\_variant,p.Val65Gly,ENST00000400198,NM\\_018011.3;ARGLU1,upstream\\_gene\\_variant,,ENST00000360629,;,regulatory\\_region\\_variant,,ENSR00000065521,;                                                                                                                                                                                                                                                                                                                                                             & C & ENSG00000134884 & ENST00000400198 & Transcript & missense\\_variant & 439/3390   & 194/822   & 65/273    & V/G & gTg/gGg &  & 1 & NA & -1 & ARGLU1  & HGNC & HGNC:25482 & protein\\_coding & YES & CCDS41906.1 & ENSP00000383059 & Q9NWB6 & A0A024RDW4 & UPI00000373ED & NM\\_018011.3    & tolerated(0.25)                & benign(0)                & 1/4   &  & Low\\_complexity\\_(Seg):seg,mobidb-lite,hmmpanther:PTHR31711:SF1,hmmpanther:PTHR31711                     & NA & NA & NA & NA & NA & NA & NA & NA & NA &  &  &  & NA & NA & NA & NA & MODERATE &  1 & SNV &  1 & NA &  & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & PASS & CAC & . & . & NA &  &  &  &  &  &  &  &  &  &      & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & 11.31 & NA & NA & NA & NA & NA & NA & NA & NA & NA &  &  &  &  & NA & NA &  & NA &  &  & NA &  & \\\\\n",
       "\t chr2:219483374  & SPEG    &  10290 & Mutect2 & GRCh38 & chr2  & 219483374 & 219483374 & + & Missense\\_Mutation & SNP & A & A & C & novel & NA & BS\\_78TQS4Y3 & BS\\_RX561Y2K & A & A & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & c.5911A>C & p.Met1971Leu & p.M1971L & ENST00000312358 & 30/41 &  57 & 49 &  8 & 25 & 25 & 0 & SPEG,missense\\_variant,p.Met1971Leu,ENST00000312358,NM\\_005876.4;AC053503.1,intron\\_variant,,ENST00000429882,;SPEG,non\\_coding\\_transcript\\_exon\\_variant,,ENST00000485813,;,regulatory\\_region\\_variant,,ENSR00000130557,;                                                                                                                                                                                                                                                                                                      & C & ENSG00000072195 & ENST00000312358 & Transcript & missense\\_variant & 6043/10782 & 5911/9804 & 1971/3267 & M/L & Atg/Ctg &  & 1 & NA &  1 & SPEG    & HGNC & HGNC:16901 & protein\\_coding & YES & CCDS42824.1 & ENSP00000311684 & Q15772 &            & UPI000066D99E & NM\\_005876.4    & tolerated(0.18)                & benign(0)                & 30/41 &  & Gene3D:1.10.510.10,hmmpanther:PTHR45065,mobidb-lite                                                    & NA & NA & NA & NA & NA & NA & NA & NA & NA &  &  &  & NA & NA & NA & NA & MODERATE & NA & SNV &  5 & NA &  & NA & NA & NA & NA & NA & NA & NA & NA & NA &  1 & PASS & CAT & . & . & NA &  &  &  &  &  &  &  &  &  & PASS & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & 9.64  & NA & NA & NA & NA & NA & NA & NA & NA & NA &  &  &  &  & NA & NA &  & NA &  &  & NA &  & \\\\\n",
       "\t chr3:51391480   & RBM15B  &  29890 & Mutect2 & GRCh38 & chr3  &  51391480 &  51391480 & + & Missense\\_Mutation & SNP & A & A & C & novel & NA & BS\\_78TQS4Y3 & BS\\_RX561Y2K & A & A & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & c.81A>C   & p.Glu27Asp   & p.E27D   & ENST00000563281 & 1/1   &  63 & 55 &  8 & 22 & 22 & 0 & RBM15B,missense\\_variant,p.Glu27Asp,ENST00000563281,NM\\_013286.4;DCAF1,downstream\\_gene\\_variant,,ENST00000423656,NM\\_014703.2;DCAF1,downstream\\_gene\\_variant,,ENST00000504652,NM\\_001171904.1;MANF,downstream\\_gene\\_variant,,ENST00000528157,NM\\_006010.5;MANF,downstream\\_gene\\_variant,,ENST00000470900,;MANF,downstream\\_gene\\_variant,,ENST00000446668,;MANF,downstream\\_gene\\_variant,,ENST00000482262,;,regulatory\\_region\\_variant,,ENSR00000152421,;                                                                            & C & ENSG00000259956 & ENST00000563281 & Transcript & missense\\_variant & 213/6641   & 81/2673   & 27/890    & E/D & gaA/gaC &  & 1 & NA &  1 & RBM15B  & HGNC & HGNC:24303 & protein\\_coding & YES & CCDS33764.1 & ENSP00000454545 & Q8NDT2 &            & UPI0000160BDE & NM\\_013286.4    & tolerated\\_low\\_confidence(0.55) & benign(0.007)            & 1/1   &  & Gene3D:3.30.70.330,hmmpanther:PTHR23189,hmmpanther:PTHR23189:SF40,mobidb-lite,Low\\_complexity\\_(Seg):seg & NA & NA & NA & NA & NA & NA & NA & NA & NA &  &  &  & NA & NA & NA & NA & MODERATE & NA & SNV & NA & NA &  & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & PASS & AAC & . & . & NA &  &  &  &  &  &  &  &  &  &      & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & 10.34 & NA & NA & NA & NA & NA & NA & NA & NA & NA &  &  &  &  & NA & NA &  & NA &  &  & NA &  & \\\\\n",
       "\t chr2:241803771  & GAL3ST2 &  64090 & Mutect2 & GRCh38 & chr2  & 241803771 & 241803771 & + & Missense\\_Mutation & SNP & A & A & C & novel & NA & BS\\_SKRY0BJ4 & BS\\_59H6VFJX & A & A & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & c.802A>C  & p.Thr268Pro  & p.T268P  & ENST00000192314 & 4/4   &  54 & 46 &  8 & 21 & 21 & 0 & GAL3ST2,missense\\_variant,p.Thr268Pro,ENST00000192314,NM\\_022134.2;AC131097.3,downstream\\_gene\\_variant,,ENST00000413820,;AC131097.1,upstream\\_gene\\_variant,,ENST00000437438,;,regulatory\\_region\\_variant,,ENSR00000133335,;                                                                                                                                                                                                                                                                                                  & C & ENSG00000154252 & ENST00000192314 & Transcript & missense\\_variant & 933/1370   & 802/1197  & 268/398   & T/P & Acc/Ccc &  & 1 & NA &  1 & GAL3ST2 & HGNC & HGNC:24869 & protein\\_coding & YES & CCDS33427.1 & ENSP00000192314 & Q9H3Q3 &            & UPI000049DF44 & NM\\_022134.2    & tolerated(0.09)                & possibly\\_damaging(0.828) & 4/4   &  & hmmpanther:PTHR14647:SF55,hmmpanther:PTHR14647,Gene3D:3.40.50.300,Pfam\\_domain:PF06990                  & NA & NA & NA & NA & NA & NA & NA & NA & NA &  &  &  & NA & NA & NA & NA & MODERATE &  1 & SNV &  1 & NA &  & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & PASS & GAC & . & . & NA &  &  &  &  &  &  &  &  &  &      & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & 6.29  & NA & NA & NA & NA & NA & NA & NA & NA & NA &  &  &  &  & NA & NA &  & NA &  &  & NA &  & \\\\\n",
       "\t chr2:29073320   & C2orf71 & 388939 & Mutect2 & GRCh38 & chr2  &  29073320 &  29073320 & + & Missense\\_Mutation & SNP & T & T & G & novel & NA & BS\\_SYWRCE3Z & BS\\_F46C86A9 & T & T & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & c.942A>C  & p.Lys314Asn  & p.K314N  & ENST00000331664 & 1/2   &  96 & 87 &  9 & 39 & 39 & 0 & C2orf71,missense\\_variant,p.Lys314Asn,ENST00000331664,NM\\_001029883.2;                                                                                                                                                                                                                                                                                                                                                                                                                                                    & G & ENSG00000179270 & ENST00000331664 & Transcript & missense\\_variant & 942/7044   & 942/3867  & 314/1288  & K/N & aaA/aaC &  & 1 & NA & -1 & C2orf71 & HGNC & HGNC:34383 & protein\\_coding & YES & CCDS42669.1 & ENSP00000332809 & A6NGG8 &            & UPI0000251DD8 & NM\\_001029883.2 & deleterious(0)                 & possibly\\_damaging(0.846) & 1/2   &  & hmmpanther:PTHR22017,Pfam\\_domain:PF15449                                                               & NA & NA & NA & NA & NA & NA & NA & NA & NA &  &  &  & NA & NA & NA & NA & MODERATE &  1 & SNV &  2 & NA &  & NA & NA & NA & NA & NA & NA & NA & NA & NA &  1 & PASS & TTT & . & . & NA &  &  &  &  &  &  &  &  &  &      & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & 8.20  & NA & NA & NA & NA & NA & NA & NA & NA & NA &  &  &  &  & NA & NA &  & NA &  &  & NA &  & \\\\\n",
       "\t chr4:56976960   & NOA1    &  84273 & Mutect2 & GRCh38 & chr4  &  56976960 &  56976960 & + & Nonsense\\_Mutation & SNP & A & A & T & novel & NA & BS\\_SYWRCE3Z & BS\\_F46C86A9 & A & A & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & c.626T>A  & p.Leu209Ter  & p.L209*  & ENST00000264230 & 1/7   & 120 & 96 & 24 & 38 & 38 & 0 & NOA1,stop\\_gained,p.Leu209Ter,ENST00000264230,NM\\_032313.3;POLR2B,upstream\\_gene\\_variant,,ENST00000314595,NM\\_000938.2;POLR2B,upstream\\_gene\\_variant,,ENST00000381227,;POLR2B,upstream\\_gene\\_variant,,ENST00000431623,;POLR2B,upstream\\_gene\\_variant,,ENST00000433463,;POLR2B,upstream\\_gene\\_variant,,ENST00000441246,NM\\_001303269.1;POLR2B,upstream\\_gene\\_variant,,ENST00000450656,;POLR2B,upstream\\_gene\\_variant,,ENST00000495311,;POLR2B,upstream\\_gene\\_variant,,ENST00000497845,;,regulatory\\_region\\_variant,,ENSR00000168712,; & T & ENSG00000084092 & ENST00000264230 & Transcript & stop\\_gained      & 1864/3415  & 626/2097  & 209/698   & L/* & tTg/tAg &  & 1 & NA & -1 & NOA1    & HGNC & HGNC:28473 & protein\\_coding & YES & CCDS3510.1  & ENSP00000264230 & Q8NC60 &            & UPI000006DAEE & NM\\_032313.3    &                                &                          & 1/7   &  & Gene3D:3.40.50.300,PROSITE\\_profiles:PS51721,hmmpanther:PTHR11089,hmmpanther:PTHR11089:SF3,cd01855      & NA & NA & NA & NA & NA & NA & NA & NA & NA &  &  &  & NA & NA & NA & NA & HIGH     &  1 & SNV &  1 & NA &  & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & PASS & CAA & . & . & NA &  &  &  &  &  &  &  &  &  &      & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & 56.37 & NA & NA & NA & NA & NA & NA & NA & NA & NA &  &  &  &  & NA & NA &  & NA &  &  & NA &  & \\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.table: 6 × 161\n",
       "\n",
       "| chrpos &lt;chr&gt; | Hugo_Symbol.y &lt;chr&gt; | Entrez_Gene_Id &lt;int&gt; | Center &lt;chr&gt; | NCBI_Build &lt;chr&gt; | Chromosome &lt;chr&gt; | Start_Position &lt;int&gt; | End_Position &lt;int&gt; | Strand &lt;chr&gt; | Variant_Classification &lt;fct&gt; | ⋯ ⋯ | oncogenic &lt;chr&gt; | LEVEL_1 &lt;lgl&gt; | LEVEL_2A &lt;lgl&gt; | LEVEL_2B &lt;chr&gt; | LEVEL_3A &lt;lgl&gt; | LEVEL_3B &lt;chr&gt; | LEVEL_4 &lt;chr&gt; | LEVEL_R1 &lt;lgl&gt; | Highest_level &lt;chr&gt; | citations &lt;chr&gt; |\n",
       "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n",
       "| chr13:106567726 | ARGLU1  |  55082 | Mutect2 | GRCh38 | chr13 | 106567726 | 106567726 | + | Missense_Mutation | ⋯ | <!----> | NA | NA | <!----> | NA | <!----> | <!----> | NA | <!----> | <!----> |\n",
       "| chr2:219483374  | SPEG    |  10290 | Mutect2 | GRCh38 | chr2  | 219483374 | 219483374 | + | Missense_Mutation | ⋯ | <!----> | NA | NA | <!----> | NA | <!----> | <!----> | NA | <!----> | <!----> |\n",
       "| chr3:51391480   | RBM15B  |  29890 | Mutect2 | GRCh38 | chr3  |  51391480 |  51391480 | + | Missense_Mutation | ⋯ | <!----> | NA | NA | <!----> | NA | <!----> | <!----> | NA | <!----> | <!----> |\n",
       "| chr2:241803771  | GAL3ST2 |  64090 | Mutect2 | GRCh38 | chr2  | 241803771 | 241803771 | + | Missense_Mutation | ⋯ | <!----> | NA | NA | <!----> | NA | <!----> | <!----> | NA | <!----> | <!----> |\n",
       "| chr2:29073320   | C2orf71 | 388939 | Mutect2 | GRCh38 | chr2  |  29073320 |  29073320 | + | Missense_Mutation | ⋯ | <!----> | NA | NA | <!----> | NA | <!----> | <!----> | NA | <!----> | <!----> |\n",
       "| chr4:56976960   | NOA1    |  84273 | Mutect2 | GRCh38 | chr4  |  56976960 |  56976960 | + | Nonsense_Mutation | ⋯ | <!----> | NA | NA | <!----> | NA | <!----> | <!----> | NA | <!----> | <!----> |\n",
       "\n"
      ],
      "text/plain": [
       "  chrpos          Hugo_Symbol.y Entrez_Gene_Id Center  NCBI_Build Chromosome\n",
       "1 chr13:106567726 ARGLU1         55082         Mutect2 GRCh38     chr13     \n",
       "2 chr2:219483374  SPEG           10290         Mutect2 GRCh38     chr2      \n",
       "3 chr3:51391480   RBM15B         29890         Mutect2 GRCh38     chr3      \n",
       "4 chr2:241803771  GAL3ST2        64090         Mutect2 GRCh38     chr2      \n",
       "5 chr2:29073320   C2orf71       388939         Mutect2 GRCh38     chr2      \n",
       "6 chr4:56976960   NOA1           84273         Mutect2 GRCh38     chr4      \n",
       "  Start_Position End_Position Strand Variant_Classification ⋯ oncogenic LEVEL_1\n",
       "1 106567726      106567726    +      Missense_Mutation      ⋯           NA     \n",
       "2 219483374      219483374    +      Missense_Mutation      ⋯           NA     \n",
       "3  51391480       51391480    +      Missense_Mutation      ⋯           NA     \n",
       "4 241803771      241803771    +      Missense_Mutation      ⋯           NA     \n",
       "5  29073320       29073320    +      Missense_Mutation      ⋯           NA     \n",
       "6  56976960       56976960    +      Nonsense_Mutation      ⋯           NA     \n",
       "  LEVEL_2A LEVEL_2B LEVEL_3A LEVEL_3B LEVEL_4 LEVEL_R1 Highest_level citations\n",
       "1 NA                NA                        NA                              \n",
       "2 NA                NA                        NA                              \n",
       "3 NA                NA                        NA                              \n",
       "4 NA                NA                        NA                              \n",
       "5 NA                NA                        NA                              \n",
       "6 NA                NA                        NA                              "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "head(overlap_sample)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [],
   "source": [
    "colnames(overlap_sample)[2] <- \"Hugo_Symbol\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [],
   "source": [
    "overlap_sample$t_VAF <- overlap_sample$t_alt_count / overlap_sample$t_depth"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<ol class=list-inline>\n",
       "\t<li>0.150943396226415</li>\n",
       "\t<li>0.140350877192982</li>\n",
       "\t<li>0.126984126984127</li>\n",
       "\t<li>0.148148148148148</li>\n",
       "\t<li>0.09375</li>\n",
       "\t<li>0.2</li>\n",
       "</ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 0.150943396226415\n",
       "\\item 0.140350877192982\n",
       "\\item 0.126984126984127\n",
       "\\item 0.148148148148148\n",
       "\\item 0.09375\n",
       "\\item 0.2\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 0.150943396226415\n",
       "2. 0.140350877192982\n",
       "3. 0.126984126984127\n",
       "4. 0.148148148148148\n",
       "5. 0.09375\n",
       "6. 0.2\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "[1] 0.1509434 0.1403509 0.1269841 0.1481481 0.0937500 0.2000000"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "head(overlap_sample$t_VAF)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [],
   "source": [
    "overlap_sample_VAF <- overlap_sample[ overlap_sample$t_VAF > 0.03,]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<ol class=list-inline>\n",
       "\t<li>55442</li>\n",
       "\t<li>162</li>\n",
       "</ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 55442\n",
       "\\item 162\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 55442\n",
       "2. 162\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "[1] 55442   162"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<ol class=list-inline>\n",
       "\t<li>55440</li>\n",
       "\t<li>162</li>\n",
       "</ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 55440\n",
       "\\item 162\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 55440\n",
       "2. 162\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "[1] 55440   162"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "dim(overlap_sample)\n",
    "\n",
    "dim(overlap_sample_VAF)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "data": {
      "image/png": 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tUuAQIECBAgQIAAAQLJCQhIyZVMhwkQ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\nJIuEAgQQQAABBBBAAAEEEHBV4BeL57MNR72pXAAAAABJRU5ErkJggg==",
      "text/plain": [
       "plot without title"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "ggplot(data = overlap_sample) + geom_histogram(aes(x = t_VAF), bins = 100)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [],
   "source": [
    "write.table(overlap_sample_VAF,\n",
    "           file = paste0(datapath,\"snv/CBTTC_maf_overlapped_3VAF.maf\"),\n",
    "           sep = \"\\t\", quote = F, row.names = F)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Add sample_id from clinical_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "-Reading\n",
      "-Validating\n",
      "-Summarizing\n",
      "--Possible FLAGS among top ten genes:\n",
      "  AHNAK\n",
      "  TTN\n",
      "-Processing clinical data\n",
      "--Missing clinical data\n",
      "-Finished in 6.302s elapsed (7.189s cpu) \n"
     ]
    }
   ],
   "source": [
    "mymaf <- read.maf(maf =  paste0(datapath,\"snv/CBTTC_maf_overlapped_3VAF.maf\"),\n",
    "                      useAll = TRUE, \n",
    "                      verbose = T,\n",
    "                      vc_nonSyn = c(\"Frame_Shift_Del\", \"Frame_Shift_Ins\", \n",
    "                                    \"Nonsense_Mutation\",\"Nonstop_Mutation\", \n",
    "                                    \"In_Frame_Del\",\"In_Frame_Ins\", \n",
    "                                    \"Missense_Mutation\"))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [],
   "source": [
    "CBTTC_mut <- getSampleSummary(mymaf)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<ol class=list-inline>\n",
       "\t<li>842</li>\n",
       "\t<li>9</li>\n",
       "</ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 842\n",
       "\\item 9\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 842\n",
       "2. 9\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "[1] 842   9"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "dim(CBTTC_mut)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A data.table: 6 × 9</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>Tumor_Sample_Barcode</th><th scope=col>Frame_Shift_Del</th><th scope=col>Frame_Shift_Ins</th><th scope=col>In_Frame_Del</th><th scope=col>In_Frame_Ins</th><th scope=col>Missense_Mutation</th><th scope=col>Nonsense_Mutation</th><th scope=col>Nonstop_Mutation</th><th scope=col>total</th></tr>\n",
       "\t<tr><th scope=col>&lt;fct&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;dbl&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>BS_8AY2GM4G</td><td>21</td><td> 21</td><td>0</td><td>1</td><td>9555</td><td>572</td><td>5</td><td>10175</td></tr>\n",
       "\t<tr><td>BS_20TBZG09</td><td>17</td><td> 31</td><td>0</td><td>1</td><td>9213</td><td>534</td><td>5</td><td> 9801</td></tr>\n",
       "\t<tr><td>BS_02YBZSBY</td><td> 9</td><td>165</td><td>0</td><td>0</td><td>8170</td><td>470</td><td>1</td><td> 8815</td></tr>\n",
       "\t<tr><td>BS_D0T6V861</td><td> 9</td><td>154</td><td>0</td><td>0</td><td>8018</td><td>457</td><td>1</td><td> 8639</td></tr>\n",
       "\t<tr><td>BS_VW4XN9Y7</td><td> 3</td><td>111</td><td>0</td><td>1</td><td>5563</td><td>266</td><td>7</td><td> 5951</td></tr>\n",
       "\t<tr><td>BS_HM5GFJN8</td><td>43</td><td> 13</td><td>3</td><td>1</td><td>1010</td><td> 35</td><td>0</td><td> 1105</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.table: 6 × 9\n",
       "\\begin{tabular}{r|lllllllll}\n",
       " Tumor\\_Sample\\_Barcode & Frame\\_Shift\\_Del & Frame\\_Shift\\_Ins & In\\_Frame\\_Del & In\\_Frame\\_Ins & Missense\\_Mutation & Nonsense\\_Mutation & Nonstop\\_Mutation & total\\\\\n",
       " <fct> & <int> & <int> & <int> & <int> & <int> & <int> & <int> & <dbl>\\\\\n",
       "\\hline\n",
       "\t BS\\_8AY2GM4G & 21 &  21 & 0 & 1 & 9555 & 572 & 5 & 10175\\\\\n",
       "\t BS\\_20TBZG09 & 17 &  31 & 0 & 1 & 9213 & 534 & 5 &  9801\\\\\n",
       "\t BS\\_02YBZSBY &  9 & 165 & 0 & 0 & 8170 & 470 & 1 &  8815\\\\\n",
       "\t BS\\_D0T6V861 &  9 & 154 & 0 & 0 & 8018 & 457 & 1 &  8639\\\\\n",
       "\t BS\\_VW4XN9Y7 &  3 & 111 & 0 & 1 & 5563 & 266 & 7 &  5951\\\\\n",
       "\t BS\\_HM5GFJN8 & 43 &  13 & 3 & 1 & 1010 &  35 & 0 &  1105\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.table: 6 × 9\n",
       "\n",
       "| Tumor_Sample_Barcode &lt;fct&gt; | Frame_Shift_Del &lt;int&gt; | Frame_Shift_Ins &lt;int&gt; | In_Frame_Del &lt;int&gt; | In_Frame_Ins &lt;int&gt; | Missense_Mutation &lt;int&gt; | Nonsense_Mutation &lt;int&gt; | Nonstop_Mutation &lt;int&gt; | total &lt;dbl&gt; |\n",
       "|---|---|---|---|---|---|---|---|---|\n",
       "| BS_8AY2GM4G | 21 |  21 | 0 | 1 | 9555 | 572 | 5 | 10175 |\n",
       "| BS_20TBZG09 | 17 |  31 | 0 | 1 | 9213 | 534 | 5 |  9801 |\n",
       "| BS_02YBZSBY |  9 | 165 | 0 | 0 | 8170 | 470 | 1 |  8815 |\n",
       "| BS_D0T6V861 |  9 | 154 | 0 | 0 | 8018 | 457 | 1 |  8639 |\n",
       "| BS_VW4XN9Y7 |  3 | 111 | 0 | 1 | 5563 | 266 | 7 |  5951 |\n",
       "| BS_HM5GFJN8 | 43 |  13 | 3 | 1 | 1010 |  35 | 0 |  1105 |\n",
       "\n"
      ],
      "text/plain": [
       "  Tumor_Sample_Barcode Frame_Shift_Del Frame_Shift_Ins In_Frame_Del\n",
       "1 BS_8AY2GM4G          21               21             0           \n",
       "2 BS_20TBZG09          17               31             0           \n",
       "3 BS_02YBZSBY           9              165             0           \n",
       "4 BS_D0T6V861           9              154             0           \n",
       "5 BS_VW4XN9Y7           3              111             0           \n",
       "6 BS_HM5GFJN8          43               13             3           \n",
       "  In_Frame_Ins Missense_Mutation Nonsense_Mutation Nonstop_Mutation total\n",
       "1 1            9555              572               5                10175\n",
       "2 1            9213              534               5                 9801\n",
       "3 0            8170              470               1                 8815\n",
       "4 0            8018              457               1                 8639\n",
       "5 1            5563              266               7                 5951\n",
       "6 1            1010               35               0                 1105"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "head(CBTTC_mut)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [],
   "source": [
    "IDlist <- read.table(paste0(manifestpath,\"CBTTC_KidsFirstIDs.txt\"),\n",
    "                        sep = \"\\t\", header = T,na.strings = \"Not Applicable\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A data.frame: 6 × 38</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>p_external_id</th><th scope=col>p_kf_id</th><th scope=col>clinical_event</th><th scope=col>normal_event1</th><th scope=col>normal_bs_1</th><th scope=col>normal_alq_1</th><th scope=col>normal_event2</th><th scope=col>normal_bs_2</th><th scope=col>normal_alq_2</th><th scope=col>normal_event3</th><th scope=col>⋯</th><th scope=col>cell_lines_rna_bs_1</th><th scope=col>cell_lines_rnaalq_1</th><th scope=col>cell_lines_rna_bs_2</th><th scope=col>cell_lines_rna_alq_2</th><th scope=col>cell_lines_rna_bs_3</th><th scope=col>cell_lines_rna_alq_3</th><th scope=col>other_bs_1</th><th scope=col>other_alq_1</th><th scope=col>X</th><th scope=col>X.1</th></tr>\n",
       "\t<tr><th scope=col>&lt;fct&gt;</th><th scope=col>&lt;fct&gt;</th><th scope=col>&lt;fct&gt;</th><th scope=col>&lt;fct&gt;</th><th scope=col>&lt;fct&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;fct&gt;</th><th scope=col>&lt;fct&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;fct&gt;</th><th scope=col>⋯</th><th scope=col>&lt;fct&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;fct&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;fct&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;fct&gt;</th><th scope=col>&lt;fct&gt;</th><th scope=col>&lt;lgl&gt;</th><th scope=col>&lt;lgl&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>C100122 </td><td>PT_98QMQZY7</td><td>7316-2724</td><td>7316-464 </td><td>BS_382HZBG4</td><td>550061</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>⋯</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr>\n",
       "\t<tr><td>C100122 </td><td>PT_98QMQZY7</td><td>7316-464 </td><td>7316-464 </td><td>BS_382HZBG4</td><td>550061</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>⋯</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr>\n",
       "\t<tr><td>C1002081</td><td>PT_8RB3EKNP</td><td>7316-4028</td><td>7316-4030</td><td>BS_6S7T92KS</td><td>717077</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>⋯</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr>\n",
       "\t<tr><td>C100491 </td><td>PT_SBHN5F68</td><td>7316-516 </td><td>7316-1995</td><td>BS_NBM9CPE4</td><td>564269</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>⋯</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr>\n",
       "\t<tr><td>C100860 </td><td>PT_WP871F5S</td><td>7316-1766</td><td>7316-1766</td><td>BS_2TZNPK1V</td><td>612657</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>⋯</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr>\n",
       "\t<tr><td>C100860 </td><td>PT_WP871F5S</td><td>7316-3336</td><td>7316-1766</td><td>BS_2TZNPK1V</td><td>612657</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>⋯</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td><td>NA</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.frame: 6 × 38\n",
       "\\begin{tabular}{r|llllllllllllllllllllllllllllllllllllll}\n",
       " p\\_external\\_id & p\\_kf\\_id & clinical\\_event & normal\\_event1 & normal\\_bs\\_1 & normal\\_alq\\_1 & normal\\_event2 & normal\\_bs\\_2 & normal\\_alq\\_2 & normal\\_event3 & normal\\_bs\\_3 & normal\\_alq\\_3 & tumor\\_dna\\_bs\\_1 & tumor\\_dna\\_alq\\_1 & tumor\\_dna\\_bs\\_2 & tumor\\_dna\\_alq\\_2 & tumor\\_rna\\_bs\\_1 & tumor\\_rna\\_alq\\_1 & tumor\\_rna\\_bs\\_2 & tumor\\_rna\\_alq\\_2 & tumor\\_rna\\_bs\\_3 & tumor\\_rna\\_alq\\_3 & cell\\_lines\\_dna\\_bs\\_1 & cell\\_lines\\_dnaalq\\_1 & cell\\_lines\\_dna\\_bs\\_2 & cell\\_lines\\_dna\\_alq\\_2 & cell\\_lines\\_dna\\_bs\\_3 & cell\\_lines\\_dna\\_alq\\_3 & cell\\_lines\\_rna\\_bs\\_1 & cell\\_lines\\_rnaalq\\_1 & cell\\_lines\\_rna\\_bs\\_2 & cell\\_lines\\_rna\\_alq\\_2 & cell\\_lines\\_rna\\_bs\\_3 & cell\\_lines\\_rna\\_alq\\_3 & other\\_bs\\_1 & other\\_alq\\_1 & X & X.1\\\\\n",
       " <fct> & <fct> & <fct> & <fct> & <fct> & <int> & <fct> & <fct> & <int> & <fct> & <fct> & <int> & <fct> & <int> & <fct> & <int> & <fct> & <int> & <fct> & <int> & <fct> & <int> & <fct> & <int> & <fct> & <int> & <fct> & <int> & <fct> & <int> & <fct> & <int> & <fct> & <int> & <fct> & <fct> & <lgl> & <lgl>\\\\\n",
       "\\hline\n",
       "\t C100122  & PT\\_98QMQZY7 & 7316-2724 & 7316-464  & BS\\_382HZBG4 & 550061 & NA & NA & NA & NA & NA & NA & BS\\_N9BF56FP & 711259 & NA & NA & BS\\_92MT680S & 717144 & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA\\\\\n",
       "\t C100122  & PT\\_98QMQZY7 & 7316-464  & 7316-464  & BS\\_382HZBG4 & 550061 & NA & NA & NA & NA & NA & NA & BS\\_JC8YV5V9 & 551198 & NA & NA & BS\\_6NRTJSYK & 746062 & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA\\\\\n",
       "\t C1002081 & PT\\_8RB3EKNP & 7316-4028 & 7316-4030 & BS\\_6S7T92KS & 717077 & NA & NA & NA & NA & NA & NA & BS\\_5KFAEMQJ & 725394 & NA & NA & BS\\_W9AT0MR7 & 724089 & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA\\\\\n",
       "\t C100491  & PT\\_SBHN5F68 & 7316-516  & 7316-1995 & BS\\_NBM9CPE4 & 564269 & NA & NA & NA & NA & NA & NA & BS\\_Q5XKTB1V & 571330 & NA & NA & BS\\_6N3AFF66 & 571424 & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA\\\\\n",
       "\t C100860  & PT\\_WP871F5S & 7316-1766 & 7316-1766 & BS\\_2TZNPK1V & 612657 & NA & NA & NA & NA & NA & NA & BS\\_R3WB0PP7 & 711144 & NA & NA & BS\\_ZA9XT151 & 717142 & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA\\\\\n",
       "\t C100860  & PT\\_WP871F5S & 7316-3336 & 7316-1766 & BS\\_2TZNPK1V & 612657 & NA & NA & NA & NA & NA & NA & BS\\_XWQTX5HH & 739810 & NA & NA & BS\\_MD3DT41J & 739926 & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA & NA\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.frame: 6 × 38\n",
       "\n",
       "| p_external_id &lt;fct&gt; | p_kf_id &lt;fct&gt; | clinical_event &lt;fct&gt; | normal_event1 &lt;fct&gt; | normal_bs_1 &lt;fct&gt; | normal_alq_1 &lt;int&gt; | normal_event2 &lt;fct&gt; | normal_bs_2 &lt;fct&gt; | normal_alq_2 &lt;int&gt; | normal_event3 &lt;fct&gt; | ⋯ ⋯ | cell_lines_rna_bs_1 &lt;fct&gt; | cell_lines_rnaalq_1 &lt;int&gt; | cell_lines_rna_bs_2 &lt;fct&gt; | cell_lines_rna_alq_2 &lt;int&gt; | cell_lines_rna_bs_3 &lt;fct&gt; | cell_lines_rna_alq_3 &lt;int&gt; | other_bs_1 &lt;fct&gt; | other_alq_1 &lt;fct&gt; | X &lt;lgl&gt; | X.1 &lt;lgl&gt; |\n",
       "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n",
       "| C100122  | PT_98QMQZY7 | 7316-2724 | 7316-464  | BS_382HZBG4 | 550061 | NA | NA | NA | NA | ⋯ | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |\n",
       "| C100122  | PT_98QMQZY7 | 7316-464  | 7316-464  | BS_382HZBG4 | 550061 | NA | NA | NA | NA | ⋯ | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |\n",
       "| C1002081 | PT_8RB3EKNP | 7316-4028 | 7316-4030 | BS_6S7T92KS | 717077 | NA | NA | NA | NA | ⋯ | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |\n",
       "| C100491  | PT_SBHN5F68 | 7316-516  | 7316-1995 | BS_NBM9CPE4 | 564269 | NA | NA | NA | NA | ⋯ | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |\n",
       "| C100860  | PT_WP871F5S | 7316-1766 | 7316-1766 | BS_2TZNPK1V | 612657 | NA | NA | NA | NA | ⋯ | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |\n",
       "| C100860  | PT_WP871F5S | 7316-3336 | 7316-1766 | BS_2TZNPK1V | 612657 | NA | NA | NA | NA | ⋯ | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |\n",
       "\n"
      ],
      "text/plain": [
       "  p_external_id p_kf_id     clinical_event normal_event1 normal_bs_1\n",
       "1 C100122       PT_98QMQZY7 7316-2724      7316-464      BS_382HZBG4\n",
       "2 C100122       PT_98QMQZY7 7316-464       7316-464      BS_382HZBG4\n",
       "3 C1002081      PT_8RB3EKNP 7316-4028      7316-4030     BS_6S7T92KS\n",
       "4 C100491       PT_SBHN5F68 7316-516       7316-1995     BS_NBM9CPE4\n",
       "5 C100860       PT_WP871F5S 7316-1766      7316-1766     BS_2TZNPK1V\n",
       "6 C100860       PT_WP871F5S 7316-3336      7316-1766     BS_2TZNPK1V\n",
       "  normal_alq_1 normal_event2 normal_bs_2 normal_alq_2 normal_event3 ⋯\n",
       "1 550061       NA            NA          NA           NA            ⋯\n",
       "2 550061       NA            NA          NA           NA            ⋯\n",
       "3 717077       NA            NA          NA           NA            ⋯\n",
       "4 564269       NA            NA          NA           NA            ⋯\n",
       "5 612657       NA            NA          NA           NA            ⋯\n",
       "6 612657       NA            NA          NA           NA            ⋯\n",
       "  cell_lines_rna_bs_1 cell_lines_rnaalq_1 cell_lines_rna_bs_2\n",
       "1 NA                  NA                  NA                 \n",
       "2 NA                  NA                  NA                 \n",
       "3 NA                  NA                  NA                 \n",
       "4 NA                  NA                  NA                 \n",
       "5 NA                  NA                  NA                 \n",
       "6 NA                  NA                  NA                 \n",
       "  cell_lines_rna_alq_2 cell_lines_rna_bs_3 cell_lines_rna_alq_3 other_bs_1\n",
       "1 NA                   NA                  NA                   NA        \n",
       "2 NA                   NA                  NA                   NA        \n",
       "3 NA                   NA                  NA                   NA        \n",
       "4 NA                   NA                  NA                   NA        \n",
       "5 NA                   NA                  NA                   NA        \n",
       "6 NA                   NA                  NA                   NA        \n",
       "  other_alq_1 X  X.1\n",
       "1 NA          NA NA \n",
       "2 NA          NA NA \n",
       "3 NA          NA NA \n",
       "4 NA          NA NA \n",
       "5 NA          NA NA \n",
       "6 NA          NA NA "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "head(IDlist)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [],
   "source": [
    "CBTTC_mut$sample_id <- NA\n",
    "CBTTC_mut$sample_id1 <- NA"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [],
   "source": [
    "CBTTC_mut$Tumor_Sample_Barcode <- as.character(CBTTC_mut$Tumor_Sample_Barcode)\n",
    "IDlist$clinical_event <- as.character(IDlist$clinical_event)\n",
    "IDlist$tumor_dna_bs_1 <- as.character(IDlist$tumor_dna_bs_1)\n",
    "IDlist$tumor_dna_bs_2 <- as.character(IDlist$tumor_dna_bs_2)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "finding sampleIds from biospecimen1 and 2 and putting them together"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "metadata": {},
   "outputs": [],
   "source": [
    "for(i in 1:nrow(CBTTC_mut)){\n",
    "    CBTTC_mut$sample_id1[i] <- IDlist$clinical_event[match(CBTTC_mut$Tumor_Sample_Barcode[i],\n",
    "                                                            IDlist$tumor_dna_bs_2)]\n",
    "}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "metadata": {},
   "outputs": [],
   "source": [
    "for(i in 1:nrow(CBTTC_mut)){\n",
    "    CBTTC_mut$sample_id[i] <- IDlist$clinical_event[match(CBTTC_mut$Tumor_Sample_Barcode[i],\n",
    "                                                            IDlist$tumor_dna_bs_1)]\n",
    "}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<ol class=list-inline>\n",
       "\t<li>842</li>\n",
       "\t<li>11</li>\n",
       "</ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 842\n",
       "\\item 11\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 842\n",
       "2. 11\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "[1] 842  11"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "dim(CBTTC_mut)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "metadata": {},
   "outputs": [],
   "source": [
    "CBTTC_mut$sample_id[!is.na(CBTTC_mut$sample_id1)] <- CBTTC_mut$sample_id1[!is.na(CBTTC_mut$sample_id1)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 43,
   "metadata": {},
   "outputs": [],
   "source": [
    "CBTTC_mut$sample_id1 <- NULL"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 44,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<ol class=list-inline>\n",
       "\t<li>796</li>\n",
       "\t<li>10</li>\n",
       "</ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 796\n",
       "\\item 10\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 796\n",
       "2. 10\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "[1] 796  10"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "dim(CBTTC_mut[!is.na(CBTTC_mut$sample_id)])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "These are the cellline entries, other_aliquots and some samples that I do not have rna"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 45,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A data.table: 46 × 10</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>Tumor_Sample_Barcode</th><th scope=col>Frame_Shift_Del</th><th scope=col>Frame_Shift_Ins</th><th scope=col>In_Frame_Del</th><th scope=col>In_Frame_Ins</th><th scope=col>Missense_Mutation</th><th scope=col>Nonsense_Mutation</th><th scope=col>Nonstop_Mutation</th><th scope=col>total</th><th scope=col>sample_id</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;chr&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>BS_HM5GFJN8</td><td>43</td><td>13</td><td>3</td><td>1</td><td>1010</td><td>35</td><td>0</td><td>1105</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_QWM9BPDY</td><td>37</td><td>12</td><td>3</td><td>1</td><td> 171</td><td> 3</td><td>0</td><td> 227</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_ERFMPQN3</td><td> 1</td><td> 7</td><td>0</td><td>0</td><td> 163</td><td> 1</td><td>0</td><td> 172</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_AFBPM6CN</td><td> 2</td><td> 0</td><td>0</td><td>0</td><td> 108</td><td> 4</td><td>0</td><td> 114</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_68TZMZH1</td><td> 0</td><td> 0</td><td>0</td><td>0</td><td>  57</td><td> 3</td><td>0</td><td>  60</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_PKZ1HWNB</td><td> 2</td><td> 1</td><td>1</td><td>0</td><td>  48</td><td> 7</td><td>0</td><td>  59</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_FJEZ3ASV</td><td> 2</td><td> 1</td><td>1</td><td>0</td><td>  46</td><td> 7</td><td>0</td><td>  57</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_JGKRN7NA</td><td> 1</td><td> 2</td><td>1</td><td>0</td><td>  40</td><td> 0</td><td>0</td><td>  44</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_X2G3JMM1</td><td> 0</td><td> 0</td><td>1</td><td>0</td><td>  43</td><td> 0</td><td>0</td><td>  44</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_RXP2ZRQT</td><td> 8</td><td> 1</td><td>1</td><td>0</td><td>  28</td><td> 2</td><td>0</td><td>  40</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_A70G7S2W</td><td> 0</td><td> 1</td><td>0</td><td>0</td><td>  32</td><td> 1</td><td>0</td><td>  34</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_XMP9XNR9</td><td> 1</td><td> 2</td><td>1</td><td>0</td><td>  26</td><td> 0</td><td>0</td><td>  30</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_TF5TTEXH</td><td> 1</td><td> 0</td><td>0</td><td>0</td><td>  24</td><td> 2</td><td>0</td><td>  27</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_853PNV7P</td><td> 2</td><td> 0</td><td>0</td><td>0</td><td>  16</td><td> 2</td><td>0</td><td>  20</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_AJAH8KG5</td><td>12</td><td> 0</td><td>0</td><td>1</td><td>   3</td><td> 2</td><td>0</td><td>  18</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_5Z4XQC9X</td><td>14</td><td> 0</td><td>0</td><td>0</td><td>   1</td><td> 0</td><td>0</td><td>  15</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_AG0BZN6F</td><td> 0</td><td> 0</td><td>0</td><td>0</td><td>  13</td><td> 0</td><td>0</td><td>  13</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_Z9NCH2XA</td><td> 0</td><td> 0</td><td>0</td><td>0</td><td>  11</td><td> 0</td><td>0</td><td>  11</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_AFAHY6HP</td><td> 1</td><td> 0</td><td>1</td><td>0</td><td>   8</td><td> 0</td><td>0</td><td>  10</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_ERAWW3H7</td><td> 1</td><td> 0</td><td>0</td><td>0</td><td>   5</td><td> 2</td><td>0</td><td>   8</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_MWXDJFWW</td><td> 5</td><td> 0</td><td>0</td><td>0</td><td>   2</td><td> 0</td><td>0</td><td>   7</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_5RD8KEED</td><td> 2</td><td> 0</td><td>0</td><td>0</td><td>   4</td><td> 0</td><td>0</td><td>   6</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_HYGK88B0</td><td> 5</td><td> 0</td><td>0</td><td>0</td><td>   1</td><td> 0</td><td>0</td><td>   6</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_S7S6YEHA</td><td> 4</td><td> 0</td><td>0</td><td>0</td><td>   2</td><td> 0</td><td>0</td><td>   6</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_CZRA594T</td><td> 0</td><td> 0</td><td>0</td><td>0</td><td>   4</td><td> 0</td><td>1</td><td>   5</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_D59VEERR</td><td> 1</td><td> 0</td><td>0</td><td>0</td><td>   4</td><td> 0</td><td>0</td><td>   5</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_16FT8V4B</td><td> 1</td><td> 1</td><td>0</td><td>0</td><td>   2</td><td> 0</td><td>0</td><td>   4</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_BM95DGCQ</td><td> 0</td><td> 0</td><td>0</td><td>0</td><td>   4</td><td> 0</td><td>0</td><td>   4</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_KSRYKCDE</td><td> 0</td><td> 0</td><td>0</td><td>0</td><td>   4</td><td> 0</td><td>0</td><td>   4</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_M659G06J</td><td> 0</td><td> 0</td><td>0</td><td>0</td><td>   3</td><td> 1</td><td>0</td><td>   4</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_MDVMT75X</td><td> 0</td><td> 2</td><td>0</td><td>0</td><td>   2</td><td> 0</td><td>0</td><td>   4</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_SFZ3A07S</td><td> 1</td><td> 0</td><td>0</td><td>0</td><td>   3</td><td> 0</td><td>0</td><td>   4</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_10HD18B8</td><td> 0</td><td> 0</td><td>0</td><td>0</td><td>   3</td><td> 0</td><td>0</td><td>   3</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_8YQGSMDK</td><td> 0</td><td> 0</td><td>0</td><td>0</td><td>   3</td><td> 0</td><td>0</td><td>   3</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_KVPJVJR7</td><td> 1</td><td> 0</td><td>0</td><td>0</td><td>   2</td><td> 0</td><td>0</td><td>   3</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_0XD58YD9</td><td> 1</td><td> 0</td><td>0</td><td>0</td><td>   1</td><td> 0</td><td>0</td><td>   2</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_36HCZ3KW</td><td> 1</td><td> 0</td><td>0</td><td>0</td><td>   1</td><td> 0</td><td>0</td><td>   2</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_3ZASRA3A</td><td> 0</td><td> 0</td><td>0</td><td>0</td><td>   2</td><td> 0</td><td>0</td><td>   2</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_A9S5HT6P</td><td> 0</td><td> 0</td><td>0</td><td>0</td><td>   2</td><td> 0</td><td>0</td><td>   2</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_AM2TZPNS</td><td> 2</td><td> 0</td><td>0</td><td>0</td><td>   0</td><td> 0</td><td>0</td><td>   2</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_17AXPP1Y</td><td> 0</td><td> 0</td><td>0</td><td>0</td><td>   1</td><td> 0</td><td>0</td><td>   1</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_9R82A3VT</td><td> 0</td><td> 0</td><td>0</td><td>0</td><td>   1</td><td> 0</td><td>0</td><td>   1</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_BS5X4H0Y</td><td> 0</td><td> 0</td><td>0</td><td>0</td><td>   1</td><td> 0</td><td>0</td><td>   1</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_K14VJ1E3</td><td> 0</td><td> 0</td><td>0</td><td>0</td><td>   1</td><td> 0</td><td>0</td><td>   1</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_PDRNE606</td><td> 0</td><td> 0</td><td>0</td><td>0</td><td>   1</td><td> 0</td><td>0</td><td>   1</td><td>NA</td></tr>\n",
       "\t<tr><td>BS_TX8C5VAJ</td><td> 0</td><td> 0</td><td>0</td><td>0</td><td>   1</td><td> 0</td><td>0</td><td>   1</td><td>NA</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.table: 46 × 10\n",
       "\\begin{tabular}{r|llllllllll}\n",
       " Tumor\\_Sample\\_Barcode & Frame\\_Shift\\_Del & Frame\\_Shift\\_Ins & In\\_Frame\\_Del & In\\_Frame\\_Ins & Missense\\_Mutation & Nonsense\\_Mutation & Nonstop\\_Mutation & total & sample\\_id\\\\\n",
       " <chr> & <int> & <int> & <int> & <int> & <int> & <int> & <int> & <dbl> & <chr>\\\\\n",
       "\\hline\n",
       "\t BS\\_HM5GFJN8 & 43 & 13 & 3 & 1 & 1010 & 35 & 0 & 1105 & NA\\\\\n",
       "\t BS\\_QWM9BPDY & 37 & 12 & 3 & 1 &  171 &  3 & 0 &  227 & NA\\\\\n",
       "\t BS\\_ERFMPQN3 &  1 &  7 & 0 & 0 &  163 &  1 & 0 &  172 & NA\\\\\n",
       "\t BS\\_AFBPM6CN &  2 &  0 & 0 & 0 &  108 &  4 & 0 &  114 & NA\\\\\n",
       "\t BS\\_68TZMZH1 &  0 &  0 & 0 & 0 &   57 &  3 & 0 &   60 & NA\\\\\n",
       "\t BS\\_PKZ1HWNB &  2 &  1 & 1 & 0 &   48 &  7 & 0 &   59 & NA\\\\\n",
       "\t BS\\_FJEZ3ASV &  2 &  1 & 1 & 0 &   46 &  7 & 0 &   57 & NA\\\\\n",
       "\t BS\\_JGKRN7NA &  1 &  2 & 1 & 0 &   40 &  0 & 0 &   44 & NA\\\\\n",
       "\t BS\\_X2G3JMM1 &  0 &  0 & 1 & 0 &   43 &  0 & 0 &   44 & NA\\\\\n",
       "\t BS\\_RXP2ZRQT &  8 &  1 & 1 & 0 &   28 &  2 & 0 &   40 & NA\\\\\n",
       "\t BS\\_A70G7S2W &  0 &  1 & 0 & 0 &   32 &  1 & 0 &   34 & NA\\\\\n",
       "\t BS\\_XMP9XNR9 &  1 &  2 & 1 & 0 &   26 &  0 & 0 &   30 & NA\\\\\n",
       "\t BS\\_TF5TTEXH &  1 &  0 & 0 & 0 &   24 &  2 & 0 &   27 & NA\\\\\n",
       "\t BS\\_853PNV7P &  2 &  0 & 0 & 0 &   16 &  2 & 0 &   20 & NA\\\\\n",
       "\t BS\\_AJAH8KG5 & 12 &  0 & 0 & 1 &    3 &  2 & 0 &   18 & NA\\\\\n",
       "\t BS\\_5Z4XQC9X & 14 &  0 & 0 & 0 &    1 &  0 & 0 &   15 & NA\\\\\n",
       "\t BS\\_AG0BZN6F &  0 &  0 & 0 & 0 &   13 &  0 & 0 &   13 & NA\\\\\n",
       "\t BS\\_Z9NCH2XA &  0 &  0 & 0 & 0 &   11 &  0 & 0 &   11 & NA\\\\\n",
       "\t BS\\_AFAHY6HP &  1 &  0 & 1 & 0 &    8 &  0 & 0 &   10 & NA\\\\\n",
       "\t BS\\_ERAWW3H7 &  1 &  0 & 0 & 0 &    5 &  2 & 0 &    8 & NA\\\\\n",
       "\t BS\\_MWXDJFWW &  5 &  0 & 0 & 0 &    2 &  0 & 0 &    7 & NA\\\\\n",
       "\t BS\\_5RD8KEED &  2 &  0 & 0 & 0 &    4 &  0 & 0 &    6 & NA\\\\\n",
       "\t BS\\_HYGK88B0 &  5 &  0 & 0 & 0 &    1 &  0 & 0 &    6 & NA\\\\\n",
       "\t BS\\_S7S6YEHA &  4 &  0 & 0 & 0 &    2 &  0 & 0 &    6 & NA\\\\\n",
       "\t BS\\_CZRA594T &  0 &  0 & 0 & 0 &    4 &  0 & 1 &    5 & NA\\\\\n",
       "\t BS\\_D59VEERR &  1 &  0 & 0 & 0 &    4 &  0 & 0 &    5 & NA\\\\\n",
       "\t BS\\_16FT8V4B &  1 &  1 & 0 & 0 &    2 &  0 & 0 &    4 & NA\\\\\n",
       "\t BS\\_BM95DGCQ &  0 &  0 & 0 & 0 &    4 &  0 & 0 &    4 & NA\\\\\n",
       "\t BS\\_KSRYKCDE &  0 &  0 & 0 & 0 &    4 &  0 & 0 &    4 & NA\\\\\n",
       "\t BS\\_M659G06J &  0 &  0 & 0 & 0 &    3 &  1 & 0 &    4 & NA\\\\\n",
       "\t BS\\_MDVMT75X &  0 &  2 & 0 & 0 &    2 &  0 & 0 &    4 & NA\\\\\n",
       "\t BS\\_SFZ3A07S &  1 &  0 & 0 & 0 &    3 &  0 & 0 &    4 & NA\\\\\n",
       "\t BS\\_10HD18B8 &  0 &  0 & 0 & 0 &    3 &  0 & 0 &    3 & NA\\\\\n",
       "\t BS\\_8YQGSMDK &  0 &  0 & 0 & 0 &    3 &  0 & 0 &    3 & NA\\\\\n",
       "\t BS\\_KVPJVJR7 &  1 &  0 & 0 & 0 &    2 &  0 & 0 &    3 & NA\\\\\n",
       "\t BS\\_0XD58YD9 &  1 &  0 & 0 & 0 &    1 &  0 & 0 &    2 & NA\\\\\n",
       "\t BS\\_36HCZ3KW &  1 &  0 & 0 & 0 &    1 &  0 & 0 &    2 & NA\\\\\n",
       "\t BS\\_3ZASRA3A &  0 &  0 & 0 & 0 &    2 &  0 & 0 &    2 & NA\\\\\n",
       "\t BS\\_A9S5HT6P &  0 &  0 & 0 & 0 &    2 &  0 & 0 &    2 & NA\\\\\n",
       "\t BS\\_AM2TZPNS &  2 &  0 & 0 & 0 &    0 &  0 & 0 &    2 & NA\\\\\n",
       "\t BS\\_17AXPP1Y &  0 &  0 & 0 & 0 &    1 &  0 & 0 &    1 & NA\\\\\n",
       "\t BS\\_9R82A3VT &  0 &  0 & 0 & 0 &    1 &  0 & 0 &    1 & NA\\\\\n",
       "\t BS\\_BS5X4H0Y &  0 &  0 & 0 & 0 &    1 &  0 & 0 &    1 & NA\\\\\n",
       "\t BS\\_K14VJ1E3 &  0 &  0 & 0 & 0 &    1 &  0 & 0 &    1 & NA\\\\\n",
       "\t BS\\_PDRNE606 &  0 &  0 & 0 & 0 &    1 &  0 & 0 &    1 & NA\\\\\n",
       "\t BS\\_TX8C5VAJ &  0 &  0 & 0 & 0 &    1 &  0 & 0 &    1 & NA\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.table: 46 × 10\n",
       "\n",
       "| Tumor_Sample_Barcode &lt;chr&gt; | Frame_Shift_Del &lt;int&gt; | Frame_Shift_Ins &lt;int&gt; | In_Frame_Del &lt;int&gt; | In_Frame_Ins &lt;int&gt; | Missense_Mutation &lt;int&gt; | Nonsense_Mutation &lt;int&gt; | Nonstop_Mutation &lt;int&gt; | total &lt;dbl&gt; | sample_id &lt;chr&gt; |\n",
       "|---|---|---|---|---|---|---|---|---|---|\n",
       "| BS_HM5GFJN8 | 43 | 13 | 3 | 1 | 1010 | 35 | 0 | 1105 | NA |\n",
       "| BS_QWM9BPDY | 37 | 12 | 3 | 1 |  171 |  3 | 0 |  227 | NA |\n",
       "| BS_ERFMPQN3 |  1 |  7 | 0 | 0 |  163 |  1 | 0 |  172 | NA |\n",
       "| BS_AFBPM6CN |  2 |  0 | 0 | 0 |  108 |  4 | 0 |  114 | NA |\n",
       "| BS_68TZMZH1 |  0 |  0 | 0 | 0 |   57 |  3 | 0 |   60 | NA |\n",
       "| BS_PKZ1HWNB |  2 |  1 | 1 | 0 |   48 |  7 | 0 |   59 | NA |\n",
       "| BS_FJEZ3ASV |  2 |  1 | 1 | 0 |   46 |  7 | 0 |   57 | NA |\n",
       "| BS_JGKRN7NA |  1 |  2 | 1 | 0 |   40 |  0 | 0 |   44 | NA |\n",
       "| BS_X2G3JMM1 |  0 |  0 | 1 | 0 |   43 |  0 | 0 |   44 | NA |\n",
       "| BS_RXP2ZRQT |  8 |  1 | 1 | 0 |   28 |  2 | 0 |   40 | NA |\n",
       "| BS_A70G7S2W |  0 |  1 | 0 | 0 |   32 |  1 | 0 |   34 | NA |\n",
       "| BS_XMP9XNR9 |  1 |  2 | 1 | 0 |   26 |  0 | 0 |   30 | NA |\n",
       "| BS_TF5TTEXH |  1 |  0 | 0 | 0 |   24 |  2 | 0 |   27 | NA |\n",
       "| BS_853PNV7P |  2 |  0 | 0 | 0 |   16 |  2 | 0 |   20 | NA |\n",
       "| BS_AJAH8KG5 | 12 |  0 | 0 | 1 |    3 |  2 | 0 |   18 | NA |\n",
       "| BS_5Z4XQC9X | 14 |  0 | 0 | 0 |    1 |  0 | 0 |   15 | NA |\n",
       "| BS_AG0BZN6F |  0 |  0 | 0 | 0 |   13 |  0 | 0 |   13 | NA |\n",
       "| BS_Z9NCH2XA |  0 |  0 | 0 | 0 |   11 |  0 | 0 |   11 | NA |\n",
       "| BS_AFAHY6HP |  1 |  0 | 1 | 0 |    8 |  0 | 0 |   10 | NA |\n",
       "| BS_ERAWW3H7 |  1 |  0 | 0 | 0 |    5 |  2 | 0 |    8 | NA |\n",
       "| BS_MWXDJFWW |  5 |  0 | 0 | 0 |    2 |  0 | 0 |    7 | NA |\n",
       "| BS_5RD8KEED |  2 |  0 | 0 | 0 |    4 |  0 | 0 |    6 | NA |\n",
       "| BS_HYGK88B0 |  5 |  0 | 0 | 0 |    1 |  0 | 0 |    6 | NA |\n",
       "| BS_S7S6YEHA |  4 |  0 | 0 | 0 |    2 |  0 | 0 |    6 | NA |\n",
       "| BS_CZRA594T |  0 |  0 | 0 | 0 |    4 |  0 | 1 |    5 | NA |\n",
       "| BS_D59VEERR |  1 |  0 | 0 | 0 |    4 |  0 | 0 |    5 | NA |\n",
       "| BS_16FT8V4B |  1 |  1 | 0 | 0 |    2 |  0 | 0 |    4 | NA |\n",
       "| BS_BM95DGCQ |  0 |  0 | 0 | 0 |    4 |  0 | 0 |    4 | NA |\n",
       "| BS_KSRYKCDE |  0 |  0 | 0 | 0 |    4 |  0 | 0 |    4 | NA |\n",
       "| BS_M659G06J |  0 |  0 | 0 | 0 |    3 |  1 | 0 |    4 | NA |\n",
       "| BS_MDVMT75X |  0 |  2 | 0 | 0 |    2 |  0 | 0 |    4 | NA |\n",
       "| BS_SFZ3A07S |  1 |  0 | 0 | 0 |    3 |  0 | 0 |    4 | NA |\n",
       "| BS_10HD18B8 |  0 |  0 | 0 | 0 |    3 |  0 | 0 |    3 | NA |\n",
       "| BS_8YQGSMDK |  0 |  0 | 0 | 0 |    3 |  0 | 0 |    3 | NA |\n",
       "| BS_KVPJVJR7 |  1 |  0 | 0 | 0 |    2 |  0 | 0 |    3 | NA |\n",
       "| BS_0XD58YD9 |  1 |  0 | 0 | 0 |    1 |  0 | 0 |    2 | NA |\n",
       "| BS_36HCZ3KW |  1 |  0 | 0 | 0 |    1 |  0 | 0 |    2 | NA |\n",
       "| BS_3ZASRA3A |  0 |  0 | 0 | 0 |    2 |  0 | 0 |    2 | NA |\n",
       "| BS_A9S5HT6P |  0 |  0 | 0 | 0 |    2 |  0 | 0 |    2 | NA |\n",
       "| BS_AM2TZPNS |  2 |  0 | 0 | 0 |    0 |  0 | 0 |    2 | NA |\n",
       "| BS_17AXPP1Y |  0 |  0 | 0 | 0 |    1 |  0 | 0 |    1 | NA |\n",
       "| BS_9R82A3VT |  0 |  0 | 0 | 0 |    1 |  0 | 0 |    1 | NA |\n",
       "| BS_BS5X4H0Y |  0 |  0 | 0 | 0 |    1 |  0 | 0 |    1 | NA |\n",
       "| BS_K14VJ1E3 |  0 |  0 | 0 | 0 |    1 |  0 | 0 |    1 | NA |\n",
       "| BS_PDRNE606 |  0 |  0 | 0 | 0 |    1 |  0 | 0 |    1 | NA |\n",
       "| BS_TX8C5VAJ |  0 |  0 | 0 | 0 |    1 |  0 | 0 |    1 | NA |\n",
       "\n"
      ],
      "text/plain": [
       "   Tumor_Sample_Barcode Frame_Shift_Del Frame_Shift_Ins In_Frame_Del\n",
       "1  BS_HM5GFJN8          43              13              3           \n",
       "2  BS_QWM9BPDY          37              12              3           \n",
       "3  BS_ERFMPQN3           1               7              0           \n",
       "4  BS_AFBPM6CN           2               0              0           \n",
       "5  BS_68TZMZH1           0               0              0           \n",
       "6  BS_PKZ1HWNB           2               1              1           \n",
       "7  BS_FJEZ3ASV           2               1              1           \n",
       "8  BS_JGKRN7NA           1               2              1           \n",
       "9  BS_X2G3JMM1           0               0              1           \n",
       "10 BS_RXP2ZRQT           8               1              1           \n",
       "11 BS_A70G7S2W           0               1              0           \n",
       "12 BS_XMP9XNR9           1               2              1           \n",
       "13 BS_TF5TTEXH           1               0              0           \n",
       "14 BS_853PNV7P           2               0              0           \n",
       "15 BS_AJAH8KG5          12               0              0           \n",
       "16 BS_5Z4XQC9X          14               0              0           \n",
       "17 BS_AG0BZN6F           0               0              0           \n",
       "18 BS_Z9NCH2XA           0               0              0           \n",
       "19 BS_AFAHY6HP           1               0              1           \n",
       "20 BS_ERAWW3H7           1               0              0           \n",
       "21 BS_MWXDJFWW           5               0              0           \n",
       "22 BS_5RD8KEED           2               0              0           \n",
       "23 BS_HYGK88B0           5               0              0           \n",
       "24 BS_S7S6YEHA           4               0              0           \n",
       "25 BS_CZRA594T           0               0              0           \n",
       "26 BS_D59VEERR           1               0              0           \n",
       "27 BS_16FT8V4B           1               1              0           \n",
       "28 BS_BM95DGCQ           0               0              0           \n",
       "29 BS_KSRYKCDE           0               0              0           \n",
       "30 BS_M659G06J           0               0              0           \n",
       "31 BS_MDVMT75X           0               2              0           \n",
       "32 BS_SFZ3A07S           1               0              0           \n",
       "33 BS_10HD18B8           0               0              0           \n",
       "34 BS_8YQGSMDK           0               0              0           \n",
       "35 BS_KVPJVJR7           1               0              0           \n",
       "36 BS_0XD58YD9           1               0              0           \n",
       "37 BS_36HCZ3KW           1               0              0           \n",
       "38 BS_3ZASRA3A           0               0              0           \n",
       "39 BS_A9S5HT6P           0               0              0           \n",
       "40 BS_AM2TZPNS           2               0              0           \n",
       "41 BS_17AXPP1Y           0               0              0           \n",
       "42 BS_9R82A3VT           0               0              0           \n",
       "43 BS_BS5X4H0Y           0               0              0           \n",
       "44 BS_K14VJ1E3           0               0              0           \n",
       "45 BS_PDRNE606           0               0              0           \n",
       "46 BS_TX8C5VAJ           0               0              0           \n",
       "   In_Frame_Ins Missense_Mutation Nonsense_Mutation Nonstop_Mutation total\n",
       "1  1            1010              35                0                1105 \n",
       "2  1             171               3                0                 227 \n",
       "3  0             163               1                0                 172 \n",
       "4  0             108               4                0                 114 \n",
       "5  0              57               3                0                  60 \n",
       "6  0              48               7                0                  59 \n",
       "7  0              46               7                0                  57 \n",
       "8  0              40               0                0                  44 \n",
       "9  0              43               0                0                  44 \n",
       "10 0              28               2                0                  40 \n",
       "11 0              32               1                0                  34 \n",
       "12 0              26               0                0                  30 \n",
       "13 0              24               2                0                  27 \n",
       "14 0              16               2                0                  20 \n",
       "15 1               3               2                0                  18 \n",
       "16 0               1               0                0                  15 \n",
       "17 0              13               0                0                  13 \n",
       "18 0              11               0                0                  11 \n",
       "19 0               8               0                0                  10 \n",
       "20 0               5               2                0                   8 \n",
       "21 0               2               0                0                   7 \n",
       "22 0               4               0                0                   6 \n",
       "23 0               1               0                0                   6 \n",
       "24 0               2               0                0                   6 \n",
       "25 0               4               0                1                   5 \n",
       "26 0               4               0                0                   5 \n",
       "27 0               2               0                0                   4 \n",
       "28 0               4               0                0                   4 \n",
       "29 0               4               0                0                   4 \n",
       "30 0               3               1                0                   4 \n",
       "31 0               2               0                0                   4 \n",
       "32 0               3               0                0                   4 \n",
       "33 0               3               0                0                   3 \n",
       "34 0               3               0                0                   3 \n",
       "35 0               2               0                0                   3 \n",
       "36 0               1               0                0                   2 \n",
       "37 0               1               0                0                   2 \n",
       "38 0               2               0                0                   2 \n",
       "39 0               2               0                0                   2 \n",
       "40 0               0               0                0                   2 \n",
       "41 0               1               0                0                   1 \n",
       "42 0               1               0                0                   1 \n",
       "43 0               1               0                0                   1 \n",
       "44 0               1               0                0                   1 \n",
       "45 0               1               0                0                   1 \n",
       "46 0               1               0                0                   1 \n",
       "   sample_id\n",
       "1  NA       \n",
       "2  NA       \n",
       "3  NA       \n",
       "4  NA       \n",
       "5  NA       \n",
       "6  NA       \n",
       "7  NA       \n",
       "8  NA       \n",
       "9  NA       \n",
       "10 NA       \n",
       "11 NA       \n",
       "12 NA       \n",
       "13 NA       \n",
       "14 NA       \n",
       "15 NA       \n",
       "16 NA       \n",
       "17 NA       \n",
       "18 NA       \n",
       "19 NA       \n",
       "20 NA       \n",
       "21 NA       \n",
       "22 NA       \n",
       "23 NA       \n",
       "24 NA       \n",
       "25 NA       \n",
       "26 NA       \n",
       "27 NA       \n",
       "28 NA       \n",
       "29 NA       \n",
       "30 NA       \n",
       "31 NA       \n",
       "32 NA       \n",
       "33 NA       \n",
       "34 NA       \n",
       "35 NA       \n",
       "36 NA       \n",
       "37 NA       \n",
       "38 NA       \n",
       "39 NA       \n",
       "40 NA       \n",
       "41 NA       \n",
       "42 NA       \n",
       "43 NA       \n",
       "44 NA       \n",
       "45 NA       \n",
       "46 NA       "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "CBTTC_mut[is.na(CBTTC_mut$sample_id)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "metadata": {},
   "outputs": [],
   "source": [
    "write.table(CBTTC_mut[!is.na(CBTTC_mut$sample_id)],\n",
    "           file = paste0(datapath,\"snv/CBTTC_mafsummary_overlapped_3VAF.txt\"),\n",
    "           sep = \"\\t\", quote = F, row.names = F)"
   ]
  }
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