Comparing SNV and SV callers
Swi9 2017 Study compares 9 SNV
- deepSNV, GATK HaplotypeCaller, GATK UnifiedGenotyper, JointSNVMix2, MuTect, SAMtools, SiNVICT, SomaticSniper, and VarScan2
- does parameter selection on some of the callers
- "GATK HP, GATK UG, and SAMtools assume that the variants are clonal, i.e. either heterozygous with a variant allele frequency of 0.5 or homozygous with a frequency of 1.0 "
- "rank-combination of deepSNV, JointSNVMix2, MuTect, SiNVICT and VarScan2 reached a sensitivity of 78% when fixing the precision at 90%, and outperformed all individual tools, where the maximum sensitivity was 71% with the same precision. "
Gor4 2016 Study compares 4 SNV
- Varscan, SomaticSniper, Strelka and MuTect2
Den9 2016 Study compares 9 SNV/indel callers
- EBCall, Mutect, Seurat, Shimmer, Indelocator, Somatic Sniper, Strelka, VarScan 2 and Virmid
Bcb8 compares 8 variant callers (2015)
Bcb3 compares 3 SV variant callers (2014)
- delly, lumpy, cm.mops
- uses 12878 trio for validation
Bro5 2014 Study compares 5 haplotyping variant callers with different mappers
- GATK HC, GATK UG, Platypus, FreeBayes, SAMTools
- vcfs here
Qia5 2014 Study compares 5 somatic mutation callers
- GATK UG with subtraction, MuTect, Strelka, SomaticSniper and VarScan2
Aus4 2013 Study compares 4 variant callers on cancer/normal exome somatic tumor data
- VarScan, SomaticSniper, JointSNVMix and Strelka
- "the proportion of somatic sites found by any other caller (at any probability threshold) improves as the candidate sets are reduced to their top calls. "
Van6 2013 Study compares 6 SNV/indel callers
- JointSNVMix, SomaticSniper, Strelka, and VarScan 2, MuTect and EBCall
CSH5 2013 Study compares 5 pipelines
- SOAP, BWA-GATK, BWA-SNVer, GNUMAP, and BWA-SAMtools
Bcb3 variant caller comparison (2013): GATK UG, GATK HC both with and without Picard and GATK adjustments, and FreeBayes
- GATK UG, GATK HC, Freebayes