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

Table 4

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

Aligner	Genotyper	Filtered TP SNVs	Filtered FP SNVs	Filtered TP indels	Filtered FP indels
Bowtie2	FreeBayes	17,504	903	481	746
Bowtie2	GATK HC	17,330	29	648	687
Bowtie2	GATK UG	19,937	49	395	338
Bowtie2	mpileup	17,049	153	402	541
Bowtie2	SNPSVM	13,983	8	—	—
BWA mem	FreeBayes	17,376	347	461	739
BWA mem	GATK HC	19,388	302	689	860
BWA mem	GATK UG	20,000	48	397	355
BWA mem	mpileup	17,070	57	403	606
BWA mem	SNPSVM	15,060	10	—	—
BWA sampe	FreeBayes	17,435	450	443	647
BWA sampe	GATK HC	19,438	214	630	725
BWA sampe	GATK UG	19,557	27	384	336
BWA sampe	mpileup	17,049	111	387	518
BWA sampe	SNPSVM	15,218	10	—
CUSHAW3	FreeBayes	16,620	7,627	362	1,294
CUSHAW3	GATK HC	16,590	2,195	665	1,551
CUSHAW3	GATK UG	17,939	2,202	357	545
CUSHAW3	mpileup	15,942	4,029	368	796
CUSHAW3	SNPSVM	—	—	—	—
MOSAIK	FreeBayes	17,177	679	458	645
MOSAIK	GATK HC	11,616	33	426	255
MOSAIK	GATK UG	16,423	42	381	224
MOSAIK	mpileup	—	—	—	—
MOSAIK	SNPSVM	4,727	3	—	—
Novoalign	FreeBayes	16,658	219	384	559
Novoalign	GATK HC	19,406	385	702	872
Novoalign	GATK UG	20,521	46	386	315
Novoalign	mpileup	16,493	62	396	579
Novoalign	SNPSVM	14,451	18	—	—