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Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

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Show all All Planned Not planned Completed Answered No status Sort by recent activity Newest post Recent activity Votes Comments
  • Accessing the resource bundle.
    • nagam surya
    • June 28, 2022 18:35
    0 votes 1 comment
  • markDuplicatesSpark running out of memory Answered
    • Matt Snyder
    • June 09, 2022 19:34
    0 votes 3 comments
  • Hard filters on VariantFiltration following HaplotypeCaller; Filter contains an illegal character Answered
    • Graeme Thorn
    • May 27, 2022 21:05
    • Edited
    0 votes 5 comments
  • HaplotypeCaller complains (in 2 different ways) about sample-name
    • Terry Jones
    • February 18, 2020 14:07
    0 votes 12 comments
  • Refseq accession number and version number in Funcotator Answered
    • TMB
    • April 26, 2022 04:13
    0 votes 4 comments
  • No results of CollectvariantCallingMetrics Answered
    • Yenan
    • November 30, 2020 07:13
    0 votes 30 comments
  • CNNScoreVariants carshes with java.lang.NullPointerException Answered
    • riederd
    • January 17, 2020 15:29
    1 vote 13 comments
  • Genomestrip: Argument with name '--ploidyMapFile' (-ploidyMapFile) is missing
    • Senwei
    • April 27, 2022 07:59
    1 vote 2 comments
  • CNNScoreVariants Issues with environment and Java version Answered
    • Kathrin B
    • April 13, 2022 15:07
    • Edited
    0 votes 6 comments
  • ApplyBQSR no positional argument is defined for this tool Answered
    • Jose Aragon
    • March 06, 2021 14:26
    0 votes 7 comments
  • Fontconfig error in the newest gatk docker image Answered
    • SkyWarrior
    • April 10, 2022 09:02
    • Edited
    0 votes 1 comment
  • Cromwell metadata of huge workflows
    • Rafal Gumienny
    • April 07, 2022 12:24
    • Edited
    0 votes 1 comment
  • vulnerability issue for gatk-package-4.2.5.0-local.jar Answered
    • John Yu
    • March 09, 2022 14:27
    0 votes 4 comments
  • Error in GenomicsDBImport: Invalid deflate block found Answered
    • Lauren Hennelly
    • February 26, 2022 20:26
    1 vote 6 comments
  • Genomestrip preprocessing error
    • chae chae
    • March 08, 2022 03:41
    • Edited
    0 votes 13 comments
  • Local WDL Mitochondria Pipeline - Import failed Answered
    • Michael
    • March 08, 2022 09:25
    • Edited
    0 votes 1 comment
  • Error in running SplitNCigarReads - htsjdk.samtools.util.RuntimeIOException Answered
    • KATHIE NGO
    • August 27, 2020 17:31
    • Edited
    0 votes 8 comments
  • GC overhead limit exceeded using Mutect2 only tumor version Answered
    • Shirliya Dadon
    • February 09, 2022 12:53
    • Edited
    0 votes 5 comments
  • Error in running GenomicsDBConfigException Answered
    • Shivangi Agarwal
    • December 20, 2021 14:51
    0 votes 12 comments
  • GATK R plots with R v4.1.2 Answered
    • Franz Gassner
    • January 24, 2022 09:36
    0 votes 3 comments
  • --tmp-dir option user error Answered
    • Brynjar Sigurðsson
    • August 10, 2020 12:22
    0 votes 13 comments
  • change the memory when running SVPreprocess
    • zzq
    • January 11, 2022 06:21
    • Edited
    0 votes 2 comments
  • Panel of Normals Documentation Answered
    • Ryan Gimple
    • April 16, 2020 17:48
    1 vote 16 comments
  • CollectRnaSeqMetrics GL000220 test not counting ribosomal reads Answered
    • rcorbett
    • December 06, 2021 18:45
    0 votes 5 comments
  • VariantsToTable positional argument eror
    • Owen Hudson
    • December 14, 2021 17:22
    0 votes 1 comment
  • GermlineCNVCaller edge case?
    • SkyWarrior
    • December 02, 2020 05:52
    • Edited
    0 votes 8 comments
  • MarkduplicatesSpark failed Answered
    • lid.zigh
    • November 23, 2021 13:44
    0 votes 3 comments
  • Merge different individual VCF
    • Linda Do
    • July 06, 2020 07:05
    1 vote 11 comments
  • Dictionary cannot have size zero error
    • Nish314
    • November 20, 2021 00:20
    • Edited
    0 votes 1 comment
  • CNNScoreVariants carshes with java.lang.NullPointerException with Python 3.8 & JDK 1.8
    • KUMAR Chandan * TCS
    • November 02, 2021 09:56
    0 votes 1 comment
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