Germline variants in Cancer

Question

[prs]

I need to design a workflow to identify pathogenic germline variants from tumor-only or tumor-normal sample data.Please suggest a workflow design or any specific tools that can be used for this purpose.

[Ram]

pathogenic

You need ClinVar, SIFT and PolyPhen2 annotations.

germline variants

Use MuTect2 with the option --genotype-germline-sites to call variants. If necessary, use --genotype-pon-sites as well.