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(requires modification to toml file for vcfanno in iobio gru backend)
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`bcbio_mv.py install` fails due to a lack of the kraken executable in the tooldir. I ran the following installation command:
```
bcbio_vm.py --datadir /bcbiotest install \
--data --tools --co…
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Hi was testing this with cwltool with the somatic workflow. Does this error look familiar?
double-posted here:
https://github.com/FarahZKhan/bcbio_test_cwlprov/issues/1#issue-550408693
```
...
…
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I am running installation with tag v2.5.1 from dev branch. There are many problems which can cause the installation to quit. I am fixing some of them, will I submit a PR ? Also I can see that many too…
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That must be me; but I can't seem to find how to pull some specific fields from a gnomAD vcf.
**gnomAD vcf file** header:
> ##fileformat=VCFv4.2
##FILTER=
##hailversion=0.2.24-9cd88d97bedd
##…
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Hi,
When I use the following file as input to vcf2db:
[working.txt](https://github.com/quinlan-lab/vcf2db/files/1395206/working.txt)
the database is created as expected.
But when I use this …
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**Version info**
- bcbio version (`bcbio_nextgen.py --version`): 1.2.5
- OS name and version (`lsb_release -ds`): "CentOS Linux release 7.9.2009 (Core)"
**To Reproduce**
Exact bcbio command you…
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Hello,
I would like to request that the tables used by GEMINI's built-in analysis tools be added into VCF2DB.
Ideally, all tables that are default loaded with the command:
$ gemini load
that…
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The little hover over local observations archive only shows the date on SNV pages. 😅
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Hi, thanks for the great tool!
Would it be possible to recognise reserved annotation names (e.g. `DB` & `SOMATIC`) and use the description given in the VCF spec for such fields (id not already pres…