In #272, support for AD files was removed from DNG and dng pileup was removed. We can continue to streamline dng call by removing support for BAM from it. However, our pileup code may still be useful, so we can move to a dng pileup command that generates a vcf with AD, PL, DP, etc. tags.
Possible Tasks
[ ] Remove support for reading BAM in dng-call
[ ] Resurrect dng pileup and have it generate VCFs from BAMs
[ ] Simplify dng-call to work at the sample level, not library level.
[ ] Provide documentation to explain how to covert technical replicates to biological replicates
In #272, support for AD files was removed from DNG and
dng pileupwas removed. We can continue to streamlinedng callby removing support for BAM from it. However, our pileup code may still be useful, so we can move to adng pileupcommand that generates a vcf with AD, PL, DP, etc. tags.Possible Tasks
dng pileupand have it generate VCFs from BAMs