A Comparison of Variant Calling Pipelines Using Genome in a Bottle as a Reference

Table 2

These are the 11 different tools used that made up the 30 (six aligners five variant callers) different pipelines. Software versions are also included to ensure reproducibility.

Tool	Type	Version	Reference
Bowtie2	Aligner	2.1.0	[14]
BWA sampe	Aligner	0.7.5a	[15]
BWA mem	Aligner	0.7.5a	[16]
CUSHAW3	Aligner	3.0.3	[17]
MOSAIK	Aligner	2.2.3	[18]
Novoalign	Aligner	3.02.07	N/A
FreeBayes	Genotyper	v9.9.2-19-g011561f	[22]
GATK HaplotypeCaller	Genotyper	2.7-2	N/A
GATK UnifiedGenotyper	Genotyper	2.7-2	[23]
SAMtools mpileup	Genotyper	0.1.19	[24]
SNPSVM	Genotyper	0.01	[25]