Evaluation of variant calling tools for large plant genome re-sequencing

BMC Bioinformatics

Table 1 Algorithms and short descriptions of the seven variant calling tools

Variant tool	Version	Algorithm	Pipelines	Default filter	Reference
FreeBayes	v1.2.0–2	Haplotype-based	FreeBayes	^b10,^m1	Garrison E, et al, 2012 [29]
FreeBayes		Bayesian			Garrison E, et al, 2012 [29]
GATK	4.0.11.0	Haplotype-based	MarkDuplicates	^b10,^m20	DePristo M, et al, 2011 [27]
		significant test	BaseRecalibrator
			HaplotypeCaller
Platypus	0.8.1	Haplotype-based	Platypus callVariants	^b20,^m20	Rimmer A, et al, 2014 [30]
Platypus		significant test			Rimmer A, et al, 2014 [30]
Samtools /mpileup	1.9	Site align-based	Samtools/mpileup	^b13,^m0	Li H, 2011 [28]
Samtools /mpileup		gt likelihoods	bcftools call		Li H, 2011 [28]
SNVer	0.5.3	Site align-based	SNVerIndividual	^b17,^m20	Wei Z, et al, 2011 [31]
SNVer	0.5.3	MAF p-value	SNVerIndividual	^f0.25,^r1,^p0.05	Wei Z, et al, 2011 [31]
VarScan	v2.3.9	Site-based	Samtools/mpileup	^b15,^m0	Koboldt D, et al, 2012 [33]
VarScan	v2.3.9	allele frequency	mpileup2snp	^f0.2,^r2,^p0.01	Koboldt D, et al, 2012 [33]
VarDict	2018	Site-based	VarDict	^b22.5,^m0	Lai Z, et al, 2016 [32]
VarDict	2018	alleles Fisher’s	var2vcf_valid	^f0.01,^r2	Lai Z, et al, 2016 [32]

^aOnly default settings were listed. ^bBQ Base quality; ^mMQ Mapping quality; ^rVR Variant containing reads or total reads containing variants (TR); ^fVF Variant frequency; ^p P-value; ^dDP Depth coverage

ISSN: 1471-2105