Closed Kurt-Hetrick closed 6 years ago
It's sambamba_v0.6.7 (used for resorting after marking duplicates) that is stripping out the PM tag from the RG header
added an issue to sambamba github repo
author determined that this was a bug and author has it as a milestone for their next release. so, for now, i'm going to use samtools reheader to fix the header...when bug is fixed, will go back to just using sambamba.
added a samtools reheader step as a fix while waiting on sambamba bug fix. issue is closed for now.
and I have no idea why...It is in the cmd line argument that gets populated and picard recognized it....really annoying. glad it is optional, but would prefer to have had it.