I’m using the Parabricks somatic pipeline (SOMATIC PIPELINE — Clara Parabricks Pipelines 3.6 documentation)
After generating vcf files, I want to add the PASS value in the FILTER field.
The problem here is that I cannot find a tool inside Parabricks that allow me to do so.
Neither I can do that outside of Parabricks using gatk FilterMutectCalls, because the somatic pipeline do not return the [output vcf].stats , that is automatically generated by gatk Mutect2.
Without that step the Parabricks Somatic Pipeline is unuseful.