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broadinstitute
Official code repository for GATK versions 4 and up
`--argument_file` is a parameter shared by many tools. It allows providing arguments in a file instead on a command line, which is very convenient when e.g., merging multiple files using...
In the documentation for the `SelectVariants` tool, it isn't clear what does `-R` do. The documentation for the `-R` is empty, it is set as an optional parameter, but both...
Dear all, I'm trying to run GenotypeGVCFs using the my_folder database created with GenomicsDBImport which should contain 222 samples. The database was created by adding progressively 10 samples at a...
This was for a spike, so this draft PR is never going to be actually merged. But having it in this format will be helpful for whoever picks the work...
Optionally extract VCFs in bgzipped compression format. Integration test - NOTE that it fails VDS validation for presumably unrelated reasons (temurin java error - presumably transient). [here](https://app.terra.bio/#workspaces/gvs-dev/GVS%20Integration/job_history/2f58faa6-918d-4d6f-9ea9-7cd00c14b216) [Here](https://app.terra.bio/#workspaces/gvs-dev/GVS%20Quickstart%20v3%20ggrant/job_history/2c4dea90-367f-4875-939a-ce0b9ae296e7) is an...
As part of my work in the Pipeline Dev team, I created 2 GATK images to address issue discussed [here](https://github.com/broadinstitute/gatk/issues/8684) (ie. having too many docker layers, we hit ACR limits...
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Official code repository for GATK versions 4 and up