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