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Variant filtering based on mapping score

Dear GATK team,

I'm writing you regarding variant filtering in the multi-sample vcf file. I have got a multi-sample vcf file containing both SNP and Indel (from human whole-genome sequencing) produced by GATK, which should be filtered based on 1) the quantile score of alignment quality for reads carrying alternative alleles, 2) the quantile score of alignment quality for reads carrying reference alleles, and also 3) chi-square value for excess or deficit of heterozygotes. Could you please help me out with this issue? If I correctly understand, here, the score of alignment is referred to the MQRankSum, yes, is it right or wrong? but how shall I compute the quantile of this score?
Regarding heterozygosity, as far as I know, there is the Phred-scaled P-value (ExcessHet) in the vcf file; but how I can calculate the chi-square value for excess or deficit of heterozygotes to filter variants based on it?

Many thanks for all your help in advance.

Answers

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