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Hi
I am not sure what the difference between the two fields `MQ` and `QUAL` is in the vcf output of VarDict as the explanations are very similar:
```
##FORMAT=
##FORMAT=
```
If the QUAL does not re…
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Hi Brad,
Recently, I used:
bcbio_nextgen.py upgrade -u development --data --tools
to update bcbio_nextgen
However, an error was occurred for pkg-config-0.28.tar.gz, the info was:
```
[localhost] …
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This came in recently when I wanted to run VarScan on an old data set.
I get errors like
```
CalledProcessError: Command 'set -o pipefail; /mnt/data/bcbio-tools/bin/samtools mpileup -f /mnt/data/bc…
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I'm trying to use `ngs_pipeline_minimal` but not getting any of the packages in the conda-based package list. Advice would be appreciated!
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Hi Brad,
I found the following new multiple errors by using the same tumor-normal pipeline that I kept running successfully recently. In the slurm file, I used --retries 3 option. Could you please hel…
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Greetings
So I managed to install cloudbiolinux successfully on BioLinux8 and Ubuntu LTS 14.04 server. I only had to install the biolinux keyring on Ubuntu server to get it to install while BioLinux…
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freebayes -parallel $variant_dir/$patient_$sample_freebayes.vcf
With or without --ploidy parameter always gives me:
could not parse ploidy
Am I missing a parameter?
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Hello,
I am trying to install an isolated version of BcBio on Ubuntu 14.04, due to no root access. However, when running the installer, I get this error:
```
[localhost] local: export CC=${CC:-which…
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When I run the CNV structural variant calling in the tumor-normal pair analysis, the error as in the title appeared. And the following detailed the missing file:
IOError: Missing CNVkit cnr file: /...…
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I have some shared filesystem IO by writing temporary files to the local disk on cluster systems with large attached local storage. I am trying to use the following section in the yaml file to use the…