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Official code repository for GATK versions 4 and up
The automatic conversion from `b37` to `hg19` yet again has resulted in a bug: On output of a compressed vcf (`.vcf.gz`), HTSJDK is unable to index the resulting file because...
The new annotation-based filtering tools make use of the utility methods in the HDF5Utils class for writing intervals, matrices, etc. to HDF5. This class currently lives in the copynumber package,...
## Documentation request I am trying to follow the germline joint variant best practices and am confused by the steps/examples and how it would work using real WGS or WXS...
This request was created from a contribution made by Joyce Anon on April 25, 2022 06:30 UTC. Link: [https://gatk.broadinstitute.org/hc/en-us/community/posts/5573282748699-Error-ShouldNeverReachHereException-FuncotationMap-in-FilterFuncotations](https://gatk.broadinstitute.org/hc/en-us/community/posts/5573282748699-Error-ShouldNeverReachHereException-FuncotationMap-in-FilterFuncotations) \-- FilterFuncotations stops with an error. The input file with the...
## Feature request ### Tool(s) or class(es) involved _Tool/class name(s), special parameters?_ [DepthOfCoverage](https://gatk.broadinstitute.org/hc/en-us/articles/360041851491-DepthOfCoverage-BETA-) ### Description Are there plans to make DepthOfCoverage multi-threaded? If not, would it be possible to require...
This request was created from a contribution made by Brian Wiley on March 18, 2022 22:33 UTC. Link: [https://gatk.broadinstitute.org/hc/en-us/community/posts/360073119131-MuTect2-annotations#community\_comment\_4797484535835](https://gatk.broadinstitute.org/hc/en-us/community/posts/360073119131-MuTect2-annotations#community_comment_4797484535835) \-- 394224746911, do you think it would be possible for Broad...
## Bug Report ### Affected tool(s) or class(es) gatk SplitNCigarReads ### Affected version(s) - gatk 4.2.6.1 ### Description I produced the bam files using STAR, and adjusted the MQ value...
We need a tool to compare multiple references and spit out a TSV (or similar) detailing what the differences are. Additionally it should be able to spit out a liftover...
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Official code repository for GATK versions 4 and up