If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Why does Mutect2 return SNPs with non-zero alt-allele freq's in the normal sample, but 0 alt reads?
I'm finding that most of the somatic SNPs that Mutect2 is inferring, have non-zero alt-alleles in the normal sample, but when I look at the AD field, they almost always have 0 reads with the alt-allele (see example below).
Is this because of the PON that I used (the one provided in the Mutect2 resource kit (my data set is too small (n=10) to generate my own))?
example below (copied from R, which was used to parse the vcf):
observedInType2AF$vcf[1:3, c( 1:7, 9:10, 42:44 ) ]
chrom pos id ref alt qual filter
794 1 9795131 . T C . PASS
12960 1 148004625 . C A . PASS