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Table 3 Criteria for calling a SNP in each of the four algorithms

From: Comparing a few SNP calling algorithms using low-coverage sequencing data

 

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