Move BAM support from call to pileup.
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reedacartwright commented
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