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HI,
Whether Optitype supports the output of 8 digits ?
I checked the paper ,but not found any information about it .
Thanks .
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Could you explain me, why it is so important?
> Note: it's important that you filter the two ends individually. Don't use the read mapper's paired-end capabilities.
As I understand, this will di…
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I'm seeing the bcbio-nextgen 1.1.9 installer get stuck trying to figure out the conda environment recipe, when these flags are used:
```
--upgrade="stable"
--datatarget="rnaseq"
--da…
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I'm trying to install the latest stable version and it's failing, something to do with a badly formatted YAML file. Here's what I'm running:
```
bcbio_path=/export/home/ncit/external/a.mizeranschi…
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https://hub.docker.com/r/fred2/optitype
So, Chai reminded me that HLA Polysolver might take forever to run, and it's old. Poorly-written perl scripts.
We discuss this, but let's use Optitype as…
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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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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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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…