Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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,