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GATK's CombineVariants, at least in the configuration I used for testing VarScan, is locale-aware, which means it will use either the decimal point or the comma depending on the running locale.
This…
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I've noticed in the last run that the pipeline saved VCF files in the output directory with the .db extension, while I expected them to be the GEMINI databases produced after the run.
It turned out …
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Hello,
I am uncertain how to correctly install and use bcbio.variation as a library from Leiningen.
I have gone through the documentation, but it didn't help much.
I have installed the lein shell s…
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Another torque request :+1:
Our informaticians are going need to be able to submit bcbio-nextgen jobs against other accounts... Currently it takes my default account but I can debit another with `qs…
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Happy to look into this, but it would be good if muTect supported running in tumour only mode or alternatively taking a vcf file instead of BAM for the normal(s).
For the first case it's sufficient …
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I've installed previous versions (last version was about 3 weeks ago) of the pipeline using the following commands in the bcbio-nextgen directory:
python setup.py build
python setup.py install
Howev…
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Hello Brad,
I tried doing variant calling with gatk and freebayes in the same analysis run using bcbio-nextgen v. 0.7.8. Content of line number `49410` mentioned at the end of the error message is th…
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Hi again,
I'm trying to use the ensemble variant calling approach and am hitting the following problem:
```
[2013-12-02 18:03] ukapdlnx117: INFO 18:03:35,710 GenotypeConcordance - Eval or Comp Rod a…
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running fab -f ./fabfile.py -H localhost install_custom:seal generates a failure:
make: Leaving directory `/tmp/pip_build_ubuntu/seal/bl/lib/seq/aligner/bwa/libbwa'
Buildfile: /tmp/pip_build_ubuntu/…
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Hi,
I am getting a error while compiling cortex. Let me know if you can help. See at the end of the text below
thanks in advance, inti
$ python2.7 bcbio_nextgen_install.py --distribution centos --nos…
inti updated
10 years ago