Table 3

Criteria for calling a SNP in each of the four algorithms
SOAPsnp Atlas-SNP2 SAMtools GATK -UGT
Quality score No Yes Yes Yes
Strand bias No Both strands must be covered by variant allele Yes Yes
Coverage limits No variant allele coverage ≥ 3 upper limits for coverage Yes No
Variant reads percentage No Heterozygous: ≥ 10% Homozygous variant: ≥ 90% No No
SNP Location No No No No

Yu and Sun

Yu and Sun BMC Bioinformatics 2013 14:274   doi:10.1186/1471-2105-14-274

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