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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

  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