For matched tumor and normal pairs, we easily get insertion and deletion counts from the output of Somatic Indel Detector in GATK. However, when we run multiple samples from the same patient, sometimes calls are made in one sample but not another, so we might not have the numbers for all samples for all indel events. We can get the deletion counts from Depth of Coverage in GATK, but retrieving insertions is trickier.
Does you have a suggestion for how to solve this problem in an automated (ie non-IGV fashion)?
Additionally, as DepthofCoverage is being retired, what do you recommend that we use for getting SNP and deletion counts?