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broadinstitute
Official code repository for GATK versions 4 and up
After the updates to the python environment made in #8561, the CNN tools are no longer functional and were deprecated. However, we may want to provide a separate environment in...
Hi, I found that even after adding --min-base-quality-score 20 to the HaplotypeCaller command line, low-quality bases are still being counted in the AD field in GVCF. **gatk version**: 4.6.0.0 (GATK4...
This PR is intended to introduce several new tools related to the CleanVcf workflow in GATK-SV, which the use of these tools being documented in https://github.com/broadinstitute/gatk-sv/pull/733. These tools are intended...
While working on #9012 I tried to update the gencode v28 datasource snippets in the Funcotator integration tests to V43. In doing so I found that it broke the MAF...
@jonn-smith
There are a number of Python-based unit tests for `NVScoreVariants` in `src/main/python/org/broadinstitute/hellbender/scorevariants/tests`, which use the standard Python `unittest` framework (https://docs.python.org/3/library/unittest.html). We should ideally hook these up to the GATK test...
no automated testing needed--just documentation edits
Three major changes here. 1. Added in logic to create the ploidy table during ingest (with necessary supporting class) and use it during extract automatically as part of the default...
Hi, It seems that for samples in which a variant was NOT detected in a cohort, that GenotypeGVCFs is putting read depth in the AD and DP FORMAT fields of...
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Official code repository for GATK versions 4 and up