It only works on bcf files, but it now produces a number of useful fields. I've put them all in INFO so we don't have to go through both tumor and normal bams at the same time, or add dummy fields for the normal sample.
That being said, it also gathers statistics on the number of overlapping read pairs, the number of discordant pairs, the number of duplex pairs, as well as such summary information on each allele.
I should also modify this to create a table of summary statistics. A "duplex" and "overlap" coverage bed tool, so to speak.
It only works on bcf files, but it now produces a number of useful fields. I've put them all in INFO so we don't have to go through both tumor and normal bams at the same time, or add dummy fields for the normal sample.
That being said, it also gathers statistics on the number of overlapping read pairs, the number of discordant pairs, the number of duplex pairs, as well as such summary information on each allele.
I should also modify this to create a table of summary statistics. A "duplex" and "overlap" coverage bed tool, so to speak.