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As said [here](https://github.com/FRED-2/OptiType/issues/92#issuecomment-494051446) - OptiType cares about read pairs.
But what about read groups?
Here is our situation - we have WGS-data with sever…
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On current system getting below HDF5 error:
Few questions:
1. Are HDF5 locks necessary for bcbio to work well in a parallel environment?
2. Currently using Lustre as scratch and have set HDF5 l…
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I am running somatic structural variant calling with 3 callers - lumpy, manta and cnvkit on paired tumor-normal exomeSeq samples. When bcbio finishes running, I don't get an ensemble vcf like I see fo…
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Hi,
I have used both razers3 and yara mapper for the aligner for Optitype and I am wondering if it would work with other aligners. Is there a specific setting / sweet spot for mismatches or clipping…
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## New feature
Hi! I need different runOptions for some of my containers, i.e. `--user root` for `fred2/optitype:latest` and `-v /var/run/docker.sock:/var/run/docker.sock` for `my/image:latest`.
…
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I have been using OptiType v1.3.1, installed using a singularity. I've trying to submit large batches of samples using a shell script, using the following command:
`singularity exec -B /home/usr:/h…
egnst updated
5 years ago
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I'm seeing a macs2 issue that I think is related to conda, popping up on one of my VMs with a clean install of bcbio:
```sh
./run_tests.sh chipseq
```
```
[2019-06-10T20:36Z] Resource request…
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Adding modules to the Snakefile
- [x] OptiType
- [x] pvacseq
- [x] Sequenza (?)
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Hi brad,
This time I am trying to do our 3rd bcbio installation on aws ec2. I am getting the below error. can you please help?
ERROR conda.core.link:_execute(502): An error occurred while instal…
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Hi guys -
Another 1.1.4 issue that is hopefully simple to address. When running the small RNA pipeline, miRge2.0 crashes like so:
```
subprocess.CalledProcessError: Command 'set -o pipefail;…