so i don't forget this. there is utility for this, i.e. if you are looking for compound heterozygote that arises due to a somatic variant...the complicating factor is that for this pipeline, no calls are from joint calling so results are sub optimal...one could conceivably joint call normals and combine somatic calls with normals, but this does not scale well because extraction of per sample normal calls from joint called vcf can be a time consuming process depending on vcf size, but having a version is better than no version, i guess.
so i don't forget this. there is utility for this, i.e. if you are looking for compound heterozygote that arises due to a somatic variant...the complicating factor is that for this pipeline, no calls are from joint calling so results are sub optimal...one could conceivably joint call normals and combine somatic calls with normals, but this does not scale well because extraction of per sample normal calls from joint called vcf can be a time consuming process depending on vcf size, but having a version is better than no version, i guess.