This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
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