From: Comparing a few SNP calling algorithms using low-coverage sequencing data
 | SOAPsnp | Atlas-SNP2 | SAMtools | GATK-UGT |
---|---|---|---|---|
Quality score | Recalibrated | Raw | Recalibrated | Recalibrated |
Machine cycle | Yes | Yes | No | Yes |
Allele type | Yes | No | No | Yes |
Duplication level | Penalty in quality score | No | No | No |
Swap-base | No | Yes | No | No |
MNP events | No | Yes | No | No |
NQS | No | Yes | No | No |
Coverage variation | No | Yes | No | No |
Base dependency | Yes | No | Yes | No |
Strand independency | No | NO | Yes | No |