VariantFiltration is incorrectly filtering variants #5916
To me, it seems VariantFiltration is incorrectly adding a filter when it clearly should not - unless I am missing something.
I am adding a filter when
However, for this critical variant, the tool is incorrectly adding a filter, when TAF is 0.55.
I have another unrelated question regarding non-mutect files. If a tool has the AD values listed under a different name (in this case AO: allele observed, instead of allele depth), how can I construct a jexl expression to filter the same?
Imagine having the same data as above, with a slightly different naming convention:
Just to follow up, I see the same issue with gatk versions 18.104.22.168 and 3.7. It seems the division operation has an issue:
It is picking up the right values, but the division is giving ZERO instead of
Thanks that helped, and also going through forums again I saw this post on jexl, and the suggested approach also worked as expected:
Re: the second question, what would be a way to retrieve non-cannonical values?
This to me suggests:
@sahilseth My apologies, I missed the last notification for this thread. For your last question, are you actually trying to retrieve genotype "DP" (in which case you should use