Currently, there are command line options to output genotype calls and arbitrary INFO and FORMAT fields, but there doesn't seem to be a way to extract the standard FILTER column (nor does the tool keep only PASS variants etc), so ant FILTER information is lost.
Currently, there are command line options to output genotype calls and arbitrary INFO and FORMAT fields, but there doesn't seem to be a way to extract the standard FILTER column (nor does the tool keep only PASS variants etc), so ant FILTER information is lost.