Table 1 SNP and indel identification parameters for VarScan, SAMtools and SeqGene in the trio family analysis
From: SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data
| Â | VarScan | SAMtools | SeqGene |
|---|---|---|---|
SNP pileup | SAMtools pileup (default, mapping quality > 10) | SAMtools pileup (default, mapping quality > 10) | SeqGene pileup (default) |
SNP filter | Coverage: > 20, 10 Average quality: > 20 Mutated bases frequency: > 25% p-value: < 1E-6 | Default filter (SAMtools varfilter) Coverage: > 20, 10 SNP quality > 20 | Coverage: > 20, 10 Bases Phred quality: > 10 Mutated bases frequency: > 25% Minor sequenced strand: > 10% |
Family-wise filter | Ignore positions with at least one 'quality control' across the family | Ignore positions with at least one 'quality control' across the family | Ignore positions with at least one 'quality control' across the family |