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Mutect variant calling the parameters for filtering

AlvaAlva SwitzerlandMember ✭✭

Hello All,
I have a couple of vcf files resulted from a batch run from the pipeline from the Mutect and I wanted to filter the output cf file based on the following parameters max_alt_alleles_in_normal_count=2 and max_alt_allele_in_normal_fraction=0.03. This I want to do as part of a comparison between results from a sample which I first ran with those parameters and second without those parameters. The first result with those parameters after in-house filters resulted in 59 variants and whereas second vcf file without those parameters resulted in 387 variants (after same in-house filtering).

Now Since I have a couple of vcf files and it takes long to process it again with the parameters I am trying filter them from result vcf files and so i tried to take out variant which has Normal allele reads >2 and Normal variant allele fraction >0.03. And still, the resulting variants doesn't match in their numbers .

Would be great if someone comment on my understanding of these parameters max_alt_allele_in_normal_fraction --isn't its frequency of alternate allele from normal sample , ie in the output vcf file its FA from Normal??
and max_alt_alleles_in_normal_count -- isn't it the Alternate allele count from Normal sample and that is AD[1] from sample Normal ??


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