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

Table 3

Raw variant statistics for the 30 pipelines, including SNVs and indels.

Aligner	Genotyper	Raw TP SNVs	Raw FP SNVs	Raw TP indels	Raw FP indels
Bowtie2	FreeBayes	23,985	73,473	806	2,482
Bowtie2	GATK HC	21,631	273	771	1,103
Bowtie2	GATK UG	25,136	2,276	418	420
Bowtie2	mpileup	21,930	1,030	734	1,414
Bowtie2	SNPSVM	17,613	47	—	—
BWA mem	FreeBayes	23,857	18,256	785	2,088
BWA mem	GATK HC	21,707	367	779	1,348
BWA mem	GATK UG	21,925	213	402	408
BWA mem	mpileup	25,081	2,129	761	1,772
BWA mem	SNPSVM	17,920	65	—	—
BWA sampe	FreeBayes	23,789	27,143	737	1,872
BWA sampe	GATK HC	21,878	263	758	1,161
BWA sampe	GATK UG	22,153	321	394	385
BWA sampe	mpileup	25,206	2,205	684	1,401
BWA sampe	SNPSVM	18,017	78	—	—
CUSHAW3	FreeBayes	23,191	53,525	624	3,310
CUSHAW3	GATK HC	19,673	14,814	751	4,727
CUSHAW3	GATK UG	19,113	13,184	360	1,005
CUSHAW3	mpileup	22,171	9,694	681	1,983
CUSHAW3	SNPSVM	—	—	—	—
MOSAIK	FreeBayes	23,373	39,203	783	3,359
MOSAIK	GATK HC	13,528	111	500	458
MOSAIK	GATK UG	17,147	76	392	284
MOSAIK	mpileup	—	—	—	—
MOSAIK	SNPSVM	14,586	8	—	—
Novoalign	FreeBayes	22,794	2,970	678	1,554
Novoalign	GATK HC	21,407	473	779	1,370
Novoalign	GATK UG	21,113	144	387	365
Novoalign	mpileup	24,512	1,861	773	1,781
Novoalign	SNPSVM	17,109	164	—	—