Platform model not added to CRAM header

Kurt-Hetrick / CIDR_WES

CIDR's production pipeline for WES and other targeted DNA sequencing projects.

0 stars 0 forks source link

Platform model not added to CRAM header #2

Closed Kurt-Hetrick closed 6 years ago

Kurt-Hetrick commented 6 years ago

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.

Kurt-Hetrick commented 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

Kurt-Hetrick commented 6 years ago

added an issue to sambamba github repo

https://github.com/biod/sambamba/issues/356

Kurt-Hetrick commented 6 years ago

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.

Kurt-Hetrick commented 6 years ago

added a samtools reheader step as a fix while waiting on sambamba bug fix. issue is closed for now.