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broadinstitute
Official code repository for GATK versions 4 and up
⛔ DO NOT MERGE this into the EchoCallset branch ⛔ just yet; it's probably better to address this bug in the current EchoCallset run by adding the two missing partitions...
# Bug Report ## Affected tool(s) or class(es) gatk `GenomicsDBImport ` `GenotypeGVCFs` ## Affected version(s) The Genome Analysis Toolkit (GATK) v4.5.0.0 ## Description Hi, Here is my situation, I'm testing...
@bbimber I've added a test to your pr https://github.com/broadinstitute/gatk/pull/8750. Should be good to merge if tests pass.
Change extract so that when we filter at the genotype level (with FT) the VCF header has the filter definition in the FORMAT field. Also minor renaming of ExtractCohort argument....
## Bug Report ### Affected tool(s) or class(es) Funcotator ### Affected version(s) 4.5.0.0 ### Description Funcotator does not select the correct transcript. It does not select the Canonical trascript ####...
## Bug Report ### Affected tool(s) or class(es) `gatk PrintReads`, `picard MarkDuplicates` ### Affected version(s) - [ ] 4.4.0.0 (htsjdk 3.0.5, picard 3.0.0) ### Description I apologize in advance if...
## Bug Report ### Affected tool(s) or class(es) ApplyVQSR, org.broadinstitute.hellbender.exceptions.GATKException ### Affected version(s) 4.5.0.0 (gatk-package-4.5.0.0-local.jar) HTSJDK Version: 4.1.0 Picard Version: 3.1.1 ### Description It Encountered input variant which isn't found...
## Bug Report ### Affected tool(s) or class(es) PathSeqPipelineSpark ### Affected version(s) GATK 4.2.2.0 ### Description I called PathSeqPipelineSpark as follows:  I confirmed my bam file has a contig...
In GATK3, when merging variants, the IDs of all the source VCFs were retained. This code path seems like it intended that, since the variantSources set is generated, but it...
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Official code repository for GATK versions 4 and up