Table 2

SNP filtering criteria for SNP discovery
Criteria used for SNP calling Cut-off values
Minimum mapped read depth to the reference ≥ 3
Maximum mapped read depth to the reference <a onClick="popup('http://www.biomedcentral.com/1471-2164/13/684/mathml/M3','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/13/684/mathml/M3">View MathML</a> + 2sa
Consensus base ratio ≥ 0.9
Mapping quality score in SAMtools ≥ 20
Removal of homopolymer SNPs with base string length ≥ 3 bp
Removal of very close SNPs with gap between contiguous SNPs < 2 bp

a<a onClick="popup('http://www.biomedcentral.com/1471-2164/13/684/mathml/M2','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/13/684/mathml/M2">View MathML</a> + 2s is the average read depth and standard deviation estimated based on the fitted extreme value distribution for each genotype separately.

Kumar et al.

Kumar et al. BMC Genomics 2012 13:684   doi:10.1186/1471-2164-13-684

Open Data