Current Mutect2 somatic variant PoN logic
Can I please confirm that this is the logic being used in the current PoN creation step:
====
Any candidate PoN site must occur in at least 2 samples (as per the default for --min-sample-count).
If the site is not in gnomad (or at negligible frequency), it's automatically treated as a candidate site for PoN inclusion.
If a site IS in gnomad at a non-negligible frequency, then it computes the probability of it being a germline variant. If the p(germline) < 0.5, then it's a candidate. (this 0.5 is manually tunable via cmd line parameter: --max-germline-probability
====
and if this is true, can we update the code documentation at:
https://github.com/broadinstitute/gatk/blob/master/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/CreateSomaticPanelOfNormals.java
to reflect that germline variants are not intended to be captured now during the PoN creation step?
-
Hi ,
The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.
Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.
We cannot guarantee a reply, however, we ask other community members to help out if you know the answer.
For context, check out our support policy.
-
Oh dear, I thought I had expunged every reference to the PoN being used to filter germline variants. I will fix it. Thanks for catching it!
-
Here's the PR: https://github.com/broadinstitute/gatk/pull/6584
Please sign in to leave a comment.
3 comments