Attention: Want an end-to-end pipelining solution for GATK Best Practices?
Could you explain how to determine gemline_risk ?
Simply, population frequency (POP_AF) and VAF(AF) seem to be the main factors.
But, some of the variants filtered by 'germline_risk' have both low AF and POP_AF at the same time.
What are the other factors to calculate probability of germline (P_GERMLINE) ?
I used panel of normals without paired normal sample.