CAGI6-Sherloc-model

The model from the SYSU-SAIL group for the CAGI6 Sherloc challenge.

This repository has been archived. See here for updates.

Input

• vcf: only the first 5 columns are required

chrom   position    ID  ref alt

• build version: hg19

• Annotation database

Demo

1. generate features

./prepare_features.sh input.vcf hg19 output

The feature file can be found at output/input.std.avinput.features-ALL.tsv

2. run prediction

./run_prediction.sh output/input.std.avinput.features-ALL.tsv

The final prediction will be at input.std.avinput.features-ALL.output.txt

Requirements

• ANNOVAR
• blast: NCBI BLAST
• MMSplice
• bedtools
• pyBigWig
• xgboost
• CrossMap
• skopt(only for training model)

How to configure config.sh

Set the keys in config.sh:

• blastp: path to the blastp program
• hg19/hg38: GRCh37(hg19)/GRCh38(hg38) reference genome
• hg19_gtf: hg19 gene annotation in GTF format
• PSSM_SPOT_PATH: path to PSSM-HHM-SPOT_DISORDER folder (decompress PSSM-HHM-SPOT_DISORDER.tgz in data/PSSM-HHM-SPOT_DISORDER)
• ROADMAP_DB: path to Roadmap ChIP-seq/DNase-seq processed data (download using the following commands in data/roadmap)

  for eid in `seq 63 113`; do
      eid=`python -c "print('E%03d' % $eid)"`
      for assay in DNase H3K27ac H3K27me3 H3K36me3 H3K4me1 H3K4me3 H3K9me3; do
          wget -c https://egg2.wustl.edu/roadmap/data/byFileType/signal/consolidated/macs2signal/pval/${eid}-${assay}.pval.signal.bigwig
      done
  done

• ENCODE_CHIPSeq_DB: path to data/encode_chipseq folder (unzip data/encode_chipseq/encode_chipseq.tgz)
• ENCODE_eCLIP_DB: path to RNA binding protein (RBP) binding sites data, tar -xf ENCODE_RBP.tar in data/eCLIP
• gtex_eQTL_loci: path to data/GTEx.eQTL.v8.hg38to19.merged.bed.gz
• gnomAD_AF_DB: path to gnomAD.v3 folder (tar -xf gnomad.v3.AF.vcf.tar in data/gnomAD.v3)
• uniprot_fasta: uniprot protein fasta file (unzip data/uniprot_human.fa.gz)
• hg19_phastCons_100way
• hg19_phyloP_100way
• hg19_phastCons_46way_primates
• hg19_phyloP_46way_primates
• hg19_phastCons_46way_vertebrate
• hg19_phyloP_46way_vertebrate
  Download the above files in bigWig format in data/ucsc/hg19 using

  wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/vertebrate.phyloP46way.bw
  wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP46way/primates.phyloP46way.bw
  wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP100way/hg19.100way.phyloP100way.bw
  wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/primates.phastCons46way.bw
  wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons46way/vertebrate.phastCons46way.bw
  wget -c http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons100way/hg19.100way.phastCons.bw  

• mmsplice_python
  install mmsplice and set mmsplice_python to the python interpreter with MMSplice installed