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## Bug Report
### Affected tool
CreateSomaticPanelOfNormals
### Affected version
Tested on version 4.1.8.0 (likely commit 3e921c6, GenomicsDB 1.3.0 #6654)
### Description
Panel of normals…
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I took my bam files that were giving this error and removed the secondary alignments (samtools view -F 256) and ran them again through Mutect2 4.1.4. I didn't get this error now. Does that mean that M…
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**Version info**
- bcbio version (bcbio_nextgen.py --version): 1.2.3
- OS name and version: Ubuntu 19.10
**To Reproduce**
bcbio_nextgen.py upgrade -u development --tools --data
**Observed b…
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DepthOfCoverage
DiagnoseTargets
From @vdauwera
It would probably make sense to write one really good tool for coverage analysis to replace these two. DoC is great at providing per-locus coverage …
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Hello,
I'm having some issues with surpyvor merge. I'm trying to process .vcf from GATK4 germline CNV caller, but their format is a bit weird. I modified it a bit and added some information to thi…
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In the news file of a structural variant software I use, I read
>Added FIX_SA and FIX_MISSING_HARD_CLIP
>FIX_SA: rewrites split read SA tags
>corrects GATK indel realignment SA tag data inconsist…
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Hi,
I have 9 sheep samples which I would like to jointly call with Lumpy express. The job dies at the 7th sample in the list. I ran each of these 9 samples individually (code below). 8 of them wor…
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Hi there - I've just encountered this issue also.
I'm running bcbio-1.1.5 through an SGE and it is difficult to upgrade to the latest version of bcbio.
This is part of the log:
> [2020-01-23T04:5…
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For @ldgauthier, upon her return from the Montreal workshop. We would like to know if this is expected behavior from HaplotypeCaller.
Researcher has uploaded read-level data to our FTP site. I've r…
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