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 |