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Compared.md

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Swi9

2017 Study

compares 9 SNV: deepSNV, GATK HaplotypeCaller, GATK UnifiedGenotyper, JointSNVMix2, MuTect, SAMtools, SiNVICT, SomaticSniper, and VarScan2 and does parameter selection on some of the callers

  • Virmid - top 4. similar to strelka, best in deep seq
  • Strelka - top 4. similar to virmid
  • EBCall - top 4. best in deep sequencing
  • Mutect - top 4
  • Seurat - largest # calls. better for high sequencing depths
  • Sniper - largest # calls, not as good in deep seq
  • Shimmer, Varscan, DeepSnV - mediocre to poor performance

Gor4

2016 Study

compares 4 SNV: Varscan, SomaticSniper, Strelka and MuTect2

  • Strelka - top 2
  • Shearwater - top 2

Den9

2016 Study

compares 9 SNV/indel callers: EBCall, Mutect, Seurat, Shimmer, Indelocator, Somatic Sniper, Strelka, VarScan 2 and Virmid

  • JointSNVMix - 2 most sens to LFV. 2 most unique FPs
  • DeepSNV - 2 most sens to LFV. 2 most unique FPs. always does better with increased depth. germline filter improves LFV
  • Mutect - germline filter improves LFV
  • Varscan2 - use minvarfreq 0.02 for LVF

Bcb8

2015

compares 8 variant callers: MuTect, VarDict, FreeBayes, Varscan, Scalpel, LUMPY, DELLY, WHAM

  • Mutect performs best

evaluated cancer tumor/normal variant calling with synthetic dataset 3 from the DREAM challenge, using multiple approaches to detect SNPs, indels and structural variants

Bcb3

2014 compares 3 SV variant callers: delly, lumpy, cm.mops

Bro5

2014 Study compares 5 haplotyping variant callers with different mappers: GATK HC, GATK UG, Platypus, FreeBayes, SAMTools

Qia5

2014 Study compares 5 somatic mutation callers: GATK UG with subtraction, MuTect, Strelka, SomaticSniper and VarScan2

  • Strelka - top 2 sens
  • Mutect - top 2 sens

Aus4

2013 Study compares 4 variant callers on cancer/normal exome somatic tumor data: VarScan, SomaticSniper, JointSNVMix and Strelka

  • JointSNVMix - inconvenient, little benefit. can have germline FPs at high depths
  • Strelka - highest TP pass rate through custom filters, lowest germline SNP FP (dbSNP presence)
  • Sniper - credible with low and medium MAF
  • Varscan2 - returns lots of germline FPs. MAF 20-75%. doesn't add anything useful

Van6

2013 Study compares 6 SNV/indel callers: JointSNVMix, SomaticSniper, Strelka, and VarScan 2, MuTect and EBCall

  • Mutect - more sensitive for LAF variants
  • Varscan2 - more sensitive for high allele frequency variants
  • EBCall - unmatched error distribution between normal references and target samples

CSH5

2013 Study compares 5 pipelines: SOAP, BWA-GATK, BWA-SNVer, GNUMAP, and BWA-SAMtools

Bcb3

variant caller comparison (2013): compares 3 pipelines: GATK UG, GATK HC both with and without Picard and GATK adjustments, and FreeBayes