Table 1 Preprocessing steps in each of the four algorithms
From: Comparing a few SNP calling algorithms using low-coverage sequencing data
| Â | SOAPsnp | Atlas-SNP2 | SAMtools | GATK |
|---|---|---|---|---|
Version | 1.03 | 1.2 | 1.1.18 | 1.6 |
Format of aligned reads | SOAP output | SAM/BAM | BAM | SAM/BAM |
Duplicate reads | Penalty | Remove using Atlas-SNP-mapper | Removed | Remove using picard [41] |
Reads with multiple-hit | Remove | Keep all hits | Keep all hits | Keep all hits |
Quality recalibration | Yes | No | Yes | Yes |
Realignment | No | No | Yes | Yes |