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Table 1 Pipelines for somatic mutation call from matched tumor-normal samples

From: isma: an R package for the integrative analysis of mutations detected by multiple pipelines

  Mutect [6] Mutect (v2) [6] Muse [22] SomaticSniper [7] Strelka [23] Varscan (v2) [8]
Variant type SNV SNV, INDELs SNV SNV SNV, INDEL SNV, INDEL
Mutation inheritance Somatic Somatic Somatic Germline, somatic, LOH Somatic Germline, somatic, LOH
Model Bayesian Bayesian Bayesian Markov Bayesian Bayesian Fisher’s exact statistics
Implementation Java Java C/C++ C Perl Java
Allelic Deptha field(s) AD AD AD BCOUNT AU:CU:GU:TU AD and RD
value(s) 2 comma separated numbers 2 comma separated numbers 2 comma separated numbers 4 comma separated numbers 4 comma separated numbers 2 numbers
License Freely available for academic, non-commercial research purposes Beta status; not available for commercial/for-profit licensing GNU GPL V2 MIT GNU General Public License Free for non-commercial use by academic, government, and non-profit/not-for-profit institutions
  1. (a) The way in which the allelic depth (number of reads supporting an allele) is encoded in VCF files is reported as an example of heterogeneity among pipeline outputs