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Platform model not added to CRAM header #2

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Kurt-Hetrick opened this issue Jun 21, 2018 · 4 comments
Closed

Platform model not added to CRAM header #2

Kurt-Hetrick opened this issue Jun 21, 2018 · 4 comments

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@Kurt-Hetrick
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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
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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
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added an issue to sambamba github repo

biod/sambamba#356

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

@Kurt-Hetrick Kurt-Hetrick mentioned this issue Oct 12, 2018
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@Kurt-Hetrick