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Filter 11 & 12 Are not Advisable in Most Cases #7

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cbird808 opened this issue Nov 6, 2019 · 0 comments
Open

Filter 11 & 12 Are not Advisable in Most Cases #7

cbird808 opened this issue Nov 6, 2019 · 0 comments

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@cbird808
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cbird808 commented Nov 6, 2019 •
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Filter 11 effectively throws out snps with too few alternate alleles, leaving SNPs with high amounts of alternate alleles. Filter 12 does the opposite.

It is based on QUAL/DP. QUAL is the phred scaled prob of an alternate allele, and is based only on alternate reads. DP is the number of reads, both alternate and ref. Thus explaining the behavior of this filter.

I believe a better approach is to compare QUAL to DPalts
@cbird808 cbird808 changed the title Filter 11 Is not Advisable Filter 11 Is not Advisable in Most Cases Nov 6, 2019
@cbird808 cbird808 changed the title Filter 11 Is not Advisable in Most Cases Filter 11 & 12 Are not Advisable in Most Cases Nov 6, 2019
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