Hi, is it possible to get the FILTER field from a gVCF into the VDS? Usually I set the genotype to “missing”, if the FILTER field is not “PASS”. I haven’t found a way to specify that when running the VDS Combiner.
This is not currently possible.
You could perform a quick filter on the gVCF beforehand, then pass the resulting outputs to the combiner.
Thanks for your quick reply. As a workaround, I will “lift” the FILTER column to the INFO field with bcftools annotate -c INFO/FT:=FILTER, which I can then later import when running the VDS combiner.