Germline risk variant calling for cancer WES

Hello all,
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,

Best Answer


Sign In or Register to comment.