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User Request:
> Removing FastQC and switching trim_galore to FastP will speed things up quite a bit and still generate the same information
FastP github repo: https://github.com/OpenGene/fastp
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Hello!
Thanks for the great pipeline!
I found a closed issue about decoys in the reference here https://github.com/bcbio/bcbio-nextgen/issues/1234
It is 2018, but still many projects are using …
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When working on a [fix for bespin-workflows/exomseq-gatk3](https://github.com/bespin-workflows/exomeseq-gatk3/pull/5) I came across documentation that says the `DP` annotation should not be used with …
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Hello,
I'm trying to run this pipeline with as many annotators as possible. However I can only output a couple of them. One that I cannot output is Mutect2 - it seems sarek skips that process, even…
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## Bug Report
### Affected tool(s) or class(es)
GATK v4.1.4.0 using FilterMutectCalls
### Affected version(s)
- [x] Latest public release version `4.1.4.0` installed from conda release `gatk4-…
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We will implement the [GATK4.0 BP](https://gatk.broadinstitute.org/hc/en-us/articles/360035531192-RNAseq-short-variant-discovery-SNPs-Indels-) workflow and skip the old recommendations for GATK 3.0.
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Dear Bcbio team,
I want to add this flag (--f1r2-tar-gz) to the caller mutect2 in my variant.yaml file.
Here's how i've done it.
details:
- algorithm:
aligner: false
mark_duplicates…
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Dear Bcbio team,
We installed bcbio new version v1.2.0 & tried to run gatk-variant pipeline. It is giving the below error.
We tried adding tools_on: gemini to yaml file. Still It is giving errors…
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scenario: someone wants to use gatk4 as a framework and add new tools. They need show on the list of tools etc. They package names are the user's, ie not org.broadinstitute.hellbender*. The way to do …