Hello!
I have some dumb questions again.
I am trying to call mutations from tumor only human samples (enriched with gene panel) from illumina. I am doing this according to this tutorial: https://gatk.broadinstitute.org/hc/en-us/articles/360035531132--How-to-Call-somatic-mutations-using-GATK4-Mutect2 .
Can i distinguish between somatic and germline mutations in this case? I know that i have to have matching normal samples to be perfectly sure, but Mutect2 says it can tell the difference. How confident can i be in Mutect2/FilterMutectCalls's predictions? And what exactly should i look at in the output vcf file? I suspect that germline mutations are those with "germline" or "panel_of_normals" (and no other words) in the "FILTER" column.
Also i do not understand what is the difference between panel of normals and allele frequency (-germline-resource) files (besides one of these contains allele frequencies) and why should we use both. I use somatic-hg38_1000g_pon.hg38.vcf.gz and somatic-hg38_af-only-gnomad.hg38.vcf.gz provided by gatk. The former has 50839 lines and the latter has 11861598 lines, and these 50839 mutations not always have large AF, and not all mutations with large AF are present in the panel of normals. Why can not we use mutations with frequencies larger than some threshold as panel of normals?
Thanks in advance.