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Hi, when I run gatk Funcotator, A USER ERROR has occurred
```
Using GATK jar /export/.conda/envs/wes/share/gatk4-4.0.5.1-0/gatk-package-4.0.5.1-local.jar
Running:
java -Dsamjdk.use_async_io_re…
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### Name of the tool
Sentieon QualCal
### Tool homepage
https://support.sentieon.com/manual/usages/general/#qualcal-algorithm
### Tool description
A Sentieon implementation of GATK4 BQSR
### Too…
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Hello,
Is it possible to upload this workflow to AWS HealthOmics? I have worked with other GATK and WARP workflows smoothly, but I'm having problems creating a workflow with this one.
Everything…
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Dear GATK developers,
Thank you very much for the tool! I recently encountered an issue while running GATK gCNV, specifically with the step GermlineCNVCaller in cohort mode. I ran the workflow usin…
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**bug report** and **feature request**
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## Feature request
### Tool(s) involved
_Tool name(s), special parameters?_
GATK
### Description
_Specify whether you want a modification of an …
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I was able to complete the processing of 500 samples in cohort mode using GATKSVPipelineBatch.wdl and would like to merge the results according to the instructions in the README.
I would like to fol…
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### Description of the bug
Hi,
I am running rnavar on a non-model organims species and I don't have vcf annotations or calibration for it. The pipeline runs after the mapping stage and it does not g…
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### Description of the bug
Merging and saveing the mapped bams fails when using GATK spark. This is due to name-sorting the reads in this case however, for merging they need to be coordinate sorted. …
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[Enter feedback here]
I tried to access gatk resources, ran into some problems, it seems that I can't access it, is there a permission limit?
https://[datasetbroadpublic.blob.core.windows.net/data…