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Table 2 Summary of the different software packages used to call SNPs

From: Breed-specific reference sequence optimized mapping accuracy of NGS analyses for pigs

Name Software Command Option
BCF SAMtools; BCFtools mpileup; call Default; −c
BCF_B SAMtools; BCFtools mpileup; call -B; −c
BCF_E SAMtools; BCFtools mpileup; call -E; −c
HAP GATK HaplotypeCaller Default
UNI GATK UnifiedGenotyper Default
UNI1 GATK UnifiedGenotyper -ploidy 1
VAR_B01 SAMtools; VarScan mpileup; mpileup2snp -B; −-min-var-freq 0.01
VAR_B10 SAMtools; VarScan mpileup; mpileup2snp -B; −-min-var-freq 0.10
VAR_B25 SAMtools; VarScan mpileup; mpileup2snp -B; −-min-var-freq 0.25
VAR_B50 SAMtools; VarScan mpileup; mpileup2snp -B; −-min-var-freq 0.50
VAR_E01 SAMtools; VarScan mpileup; mpileup2snp -E; −-min-var-freq 0.01
VAR_E10 SAMtools; VarScan mpileup; mpileup2snp -E; −-min-var-freq 0.10
VAR_E25 SAMtools; VarScan mpileup; mpileup2snp -E; −-min-var-freq 0.25
VAR_E50 SAMtools; VarScan mpileup; mpileup2snp -E; −-min-var-freq 0.50
VAR01 SAMtools; VarScan mpileup; mpileup2snp Default; −-min-var-freq 0.01
VAR10 SAMtools; VarScan mpileup; mpileup2snp Default; −-min-var-freq 0.10
VAR25 SAMtools; VarScan mpileup; mpileup2snp Default; −-min-var-freq 0.25
VAR50 SAMtools; VarScan mpileup; mpileup2snp Default; −-min-var-freq 0.50