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Germline risk variant calling for cancer WES
Being relatively new to NGS analysis techniques I recently build a pipeline for calling somatic variants in matched Tumor/Normal cancer Exome data.
I recently decided to analyze the "germline risk variants" as well.
Currently I'm calling germline variants separately using (HC) and then hard-filtering using the VariantFilter tool(since I only have a few examples at the moment) and annotating the variants with Oncotator.
However, I realized that Mutect2-Oncotator output has a column titled "germline_risk", would this serve the same purpose? If so, would this mean the separate germline variant calling is useless?
Thanks beforehand for the answers,