Dear GATK team,
We are working with tumor-only samples using Mutect2 and FilterMutectCalls and we are analyzing confirmed PCR variants when changing the panel of normals.
Unfortunately, we do not have enough normal samples to create our own panel of normals so we performed the following analysis using two different panels of normals:
1. Your publicly available panel of normals recommended in https://gatk.broadinstitute.org/hc/en-us/community/posts/360056302271-Mutect2-
2. Fake panel of normals containing only one sample for testing purposes
When using our one-sample panel of normals, real variants appear with PASS and when using your publicly available panel of normals they disappear from VCF file. Could you help us solve this issue?
I attach IGV screenshot with both analysis performed:
A panel of normal is highly recommended in Best Practices and we understood germline filtering only relies on germline resource (https://gatkforums.broadinstitute.org/gatk/discussion/24183/pon-causing-missed-somatic-variant-call-with-mutect2). Thus, we could not solve why using your panel of normals leads us to losing real variants confirmed by PCR, considering them artifacts.
Thanks in advance for your kind help!
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