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Official code repository for GATK versions 4 and up
## Bug Report ### Affected tool(s) or class(es) VariantRecalibrator ### Affected version(s) - [X] Latest public release version [4.5.0.0] - [ ] Latest master branch as of [date of test?]...
As mentioned in https://gatk.broadinstitute.org/hc/en-us/community/posts/22723956489371-Link-checking-for-the-GATK-documentation, many of the links in the HaplotypeCaller tool docs are broken.
Hi GATK, I have done the steps, i.e., 1)haplotypecaller 2)combineGVCF 3) GenotypeGVCF. Now I am interested in performing the allele matching between two samples, like whether the alleles are the...
@droazen I noticed we never removed the beta marker from this. I think it should be considered no longer beta given it's pretty intensive use for the last several years.
I am running `gatk GenotypeGVCFs` and want to get output for all genomic sites. I was expecting the output to include parameters like QUAL and mapping quality (MQ) for invariant...
A user reports in https://gatk.broadinstitute.org/hc/en-us/community/posts/21559395629723-haplotycaller-alleles-arrayIndexOutofBoundsException that they are running into an edge-case `ArrayIndexOutOfBoundsException` in `TandemRepeat.getNumTandemRepeatUnits()` while running `HaplotypeCaller` in `--alleles` mode to re-genotype a 175bp deletion: ``` java.lang.ArrayIndexOutOfBoundsException: arraycopy: source...
## Bug Report ### Affected tool(s) or class(es) `SAMRecord` from `GATKRead` ### Affected version(s) - [x] Latest master branch as of January 30, 2024 ### Description When I run a...
When I use gatk to CombineGVCFs, the following error occurs: "Cannot read file because no suitable codecs found". How can I solve this problem？
## Feature request ### Tool(s) or class(es) involved This is a request for a new tool `GencodeRegionsAsBED` ### Description Given a GENCODE gtf, create a BED file with the region...
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Official code repository for GATK versions 4 and up