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

BMC Bioinformatics

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

		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 Depth^a	field(s)	AD	AD	AD	BCOUNT	AU:CU:GU:TU	AD and RD
Allelic Depth^a	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

(^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

ISSN: 1471-2105