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#109 highlighted some issues: namely, which tools to support tumor/paired calls.
There is a comprehensive list on BioStars (http://www.biostars.org/p/19104/), so the plan would be to evaluate which o…
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VarScan (v 2.4.2) uses the invalid Alt field character "-" to signify a deletion, as in Ref=C, Alt= -T, which should instead show two Ref bases and only the T as the Alt base. I was surprised that bc…
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Hello,
I am trying to install bcbio on Temasek Life science HPC in Singapore and got the below error,
The following packages will be DOWNGRADED due to dependency conflicts:
fontconfig: …
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I'm not sure this is a bug, precisely, but it may need some explanation.
When I give a s3 bucket as outputdir in the config file, the run will fail if you did not create a 'directory' inside the buck…
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Help.
I ran a clean update and cleared tmp folder, still getting the same error.
update:
sudo bcbio_nextgen.py upgrade -u development --tools --data --datatarget vep --datatarget gemini --dat…
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Rationale for this issue: a few days ago the wet lab people were validating some of the mutations I had found, and while they correctly validated them, it turned out they weren't somatic, but germline…
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Would it be possible to make maf2maf work for the standard tab delimited varscan output? VarScan output is not the same as MAF, but it's similar, as it's tab delimited. Positions are the same as in th…
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I'm very new to linux and installs such as this, sorry if this is a silly question, I do feel like I'm missing something obvious. I keep getting a conda lock error. I've tried installing multiple time…
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`git clone https://github.com/jeremiahsavage/cwl_python_command.git`
cwltool:
```
(cwl) [jeremiah@localhost ~]$ cwltool cwl_python_command/get_uuid.cwl cwl_python_command/get_uuid.json
/home/je…
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Hi!
I spotted an error message in the flowing by text output while running a paired tumor-normal analysis:
Use of uninitialized value $sample in concatenation (.) or string at /usr/local/bin/var2vc…