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Hello bcbio folks,
I am having trouble understanding the rationale behind the SpvFreq filter in varscan.py:
It says:
> """Filter VarScan calls based on the SPV value and frequency.
Removes c…
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ONC58 has stalled again – no varscan vcf’s or coverage reports
mneat updated
6 years ago
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I am receiving an error running the README.md example that is due to not have parenthetical :
`Error in .::stats : unused argument (na.omit)`
```
library(magrittr)
library(antigen.garnish)
…
ghost updated
6 years ago
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Hi!
First of all, thank you for this awesome tool!
I would like to know if I could use SomaticSeq for target panel sequencing data. Concretely, I am managing Ion Torrent panel data. We have ~50 pati…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/sandmanns/appreci8R
Confirm the following by edit…
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This looks great so far, but I believe that the macOS installation instructions need an update. As described [here](https://github.com/Homebrew/homebrew-science/issues/6365), homebrew/science is unfor…
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I try to merge 3 variant calling but unfortunately I have this error:
```
/opt/bcbio.variation.recall/bcbio-variation-recall ensemble -c 1 -n 1 --names somaticsniper,varscan 436.merge.bcbio.vcf.g…
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During VEP annotation, I get the following error (bcbio-nextgen.log):
https://gist.github.com/leiendeckerlu/ad795a26dcfc914e3ddfed2ab1c329cc
Maybe related to this https://github.com/chapmanb/bcb…
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Hi,
Not sure if this is intended, but I noticed that executables from some of the conda environments aren't getting symlinked into `bcbio_nextgen/tools/bin`. The ones from the bcbio-vm environment …
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I have a PR coming for the reheadering which will fix the vcf reheadering. I am however getting this error:
```
[varscan.snp.genome.wustl.edu.TCGA-W5-AA33.vcf] VCF header validation error: SAMPLE hea…