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FuncotateSegments java.lang.IllegalArgumentException: Invalid interval in FuncotateSegments

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This request was created from a contribution made by tc on February 09, 2022 17:49 UTC. Link: [https://gatk.broadinstitute.org/hc/en-us/community/posts/4418364848795-java-lang-IllegalArgumentException-Invalid-interval-in-FuncotateSegments](https://gatk.broadinstitute.org/hc/en-us/community/posts/4418364848795-java-lang-IllegalArgumentException-Invalid-interval-in-FuncotateSegments) \-- Hi, I tried to annotated a called segment file after following...

GATKSupportTeam

GATK version: gatk-4.2.3 I have two bam files: `Tumor.bam` is cfDNA data, and `Normal.bam` were reads from white blood cells. There's a variant C to G at `chr7:116795782` (hg38), I...

wangshun1121

DocumentationGenerationIntegrationTest fails mysteriously

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This came up on PR #6351 after a rebase. The branch passes all tests locally (verified on my laptop and on @cmnbroad's) but fails `DocumentationGenerationIntegrationTest.documentationSmokeTest` in the docker integration CI...

davidbenjamin

discordant output between MarkDuplicates and MarkDuplicatesSpark

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## Bug Report ### Affected tool(s) or class(es) gatk MarkDuplicatesSpark ### Affected version(s) - GATK 4.2.6.1 - Spark 3.2.1 ### Description File sizes are different between MarkDuplicates and MarkDuplicatesSpark (run...

williambrandler

Clear guidelines needed for GermlineCNVCaller expected runtime, cpu usage and memory usage

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## Documentation request ### Tool(s) or class(es) involved GermlineCNVCaller ### Description I'm trying to get a pipeline running to call germline CNVs on small cohorts (20-40) PCR free whole genome...

tfenne

Funcotator IllegalArgumentException

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This request was created from a contribution made by Jay Singh on May 09, 2020 12:47 UTC. Link: https://gatk.broadinstitute.org/hc/en-us/community/posts/360062649991-java-lang-IllegalArgumentException-Invalid-interval-Contig-chr1-start-9-end-10464 -- Can you please provide a) GATK version used - **gatk-4.1.7.0**...

GATKSupportTeam

remove AC AN AF since they get recalculated anyway

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and are wrong because of the GT filtering hack

RoriCremer

Callset stats [VS-388] [VS-560]

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RoriCremer

BAM versus CRAM index extension pattern

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GATK Version 4.0.9.0 What is the issue: When using the -OBI flag in e.g. ApplyBQSR, GATK uses an inconsistent pattern for adding index extensions When using BAM format as output:...

marchoeppner

reproduction problem of HaplotypeCaller when different interval split

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Hi. The VCF output file of HaplotypeCaller is not same when different interval split. It seems that smaller region will product more var into vcf file. split1:chr unit 5,089,533 var...

wangyugui