so that all the files in the sample sheet can be obtained from the cram header, even though both the target and titv bed files have nothing to do with cram generation. they are used for various things downstream...there is a limitation to this, but i'm going to go ahead and do this for now...it really would be better if i only included the bait bed file since that directly affects cram generation, but populating the cram header with the other bed files doesn't necessarily hurt...just if the downstream files (gvcf, titv metrics, etc) end up using a different bed than in the cram header it could get a little confusing, but the vcf header should retain what the exact bed file was used for whatever analysis to offset this.
Kurt-Hetrick
commented
6 years ago
so that all the files in the sample sheet can be obtained from the cram header, even though both the target and titv bed files have nothing to do with cram generation. they are used for various things downstream...there is a limitation to this, but i'm going to go ahead and do this for now...it really would be better if i only included the bait bed file since that directly affects cram generation, but populating the cram header with the other bed files doesn't necessarily hurt...just if the downstream files (gvcf, titv metrics, etc) end up using a different bed than in the cram header it could get a little confusing, but the vcf header should retain what the exact bed file was used for whatever analysis to offset this.