Table 1

SNP and indel identification parameters for VarScan, SAMtools and SeqGene in the trio family analysis

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


Deng BMC Bioinformatics 2011 12:267   doi:10.1186/1471-2105-12-267

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