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 |