Table 2 Filters applied on raw SNP and INDELS in mutation analysis.
From: In-silico identification and prioritization of therapeutic targets of asthma
Parameter | Function | Threshold |
|---|---|---|
QuaByDepth (QD) | QD is the variant quality divided by unfiltered depth of non-hom-ref samples | > 2 |
FisherStrand (FS) | Strand Bias tells us whether the alternate allele was seen more or less often on the forward or reverse strand than the reference allele | < 60 |
RMSMappingQuality (MQ) | It is the root mean square mapping quality over all the reads at the site | > 40 |
MappingQualityRankSum Test (MQRankSum) | It compares the mapping qualities of the reads supporting the reference allele and the alternate allele | > − 12.5 |
ReadPosRankSum Test (ReadPosRankSum) | It compares whether the positions of the reference and alternate alleles are different within the reads | > − 8 |
StrandOddsRatio (SOR) | Strand Odds is another way to estimate strand bias using a test similar to the symmetric odds ratio test | < 4 |
