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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 comments Newest post Recent activity Votes Comments
  • Custom ReadFilter to ignore malformed reads ?
    • Yokofakun
    • March 21, 2020 13:26
    0 votes 2 comments
  • GATK4 HaplotypeCaller - read is malformed
    • Yi-Sian Lin
    • March 19, 2020 05:21
    • Edited
    0 votes 2 comments
  • CreateSomaticPanelOfNormals fails
    • Dieter Best
    • February 28, 2020 23:46
    0 votes 2 comments
  • Out of memory error using OpenJDK vs Oracle JDK for CNV-LOH
    • Jose Arcadio Buendia
    • February 28, 2020 01:53
    • Edited
    2 votes 2 comments
  • Delete <NON_REF> from VCF
    • ValeriyaVS
    • February 26, 2020 08:02
    0 votes 2 comments
  • BI and BD tags.
    • Semen Leyn
    • February 17, 2020 19:44
    0 votes 2 comments
  • Cannot get AddOrReplaceReadGroups to run
    • Robert Butler
    • February 12, 2020 21:20
    0 votes 2 comments
  • GATK on Oracle Cloud Infrastructure
    • Marcelo Bicudo
    • February 06, 2020 21:18
    0 votes 2 comments
  • Where to find old discussion
    • Khalil Jahed
    • January 22, 2020 16:04
    0 votes 2 comments
  • Feature request: Restore the StrandAlleleCount annotation from GATK3
    • johnma
    • January 12, 2020 16:24
    0 votes 2 comments
  • Accessing the resource bundle.
    • nagam surya
    • June 28, 2022 18:35
    0 votes 1 comment
  • 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
  • Local WDL Mitochondria Pipeline - Import failed Answered
    • Michael
    • March 08, 2022 09:25
    • Edited
    0 votes 1 comment
  • VariantsToTable positional argument eror
    • Owen Hudson
    • December 14, 2021 17:22
    0 votes 1 comment
  • 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
  • CalculateContamination 4.1.2.0 org.apache.commons.math3.exception.TooManyEvaluationsException
    • 陈星瀚
    • October 29, 2021 09:21
    0 votes 1 comment
  • Hi Can you please point me to the chain file for human_g1k_v37_decoy to hg19 conversion Answered
    • smk_84
    • July 06, 2021 20:48
    • Edited
    0 votes 1 comment
  • Funcotator missing cDNA, Codon, and Protein Change for some chromosomes Answered
    • Robert Bremel
    • June 05, 2021 01:44
    0 votes 1 comment
  • GenomicsDBImport - A USER ERROR has occurred: Failed to create reader from file: 2.0
    • Jared Johnson
    • May 07, 2021 20:44
    0 votes 1 comment
  • How do I keep a glob from copying a file in Cromwell / WDL
    • Gregory Dougherty
    • March 09, 2021 00:24
    0 votes 1 comment
  • How to Fix the follow ValidateSamFile error ?
    • Luis Enrique Romero Cruz
    • March 06, 2021 03:51
    0 votes 1 comment
  • BaseRecalibrator on MT .bam files
    • Sharon Cox
    • February 19, 2021 09:48
    • Edited
    0 votes 1 comment
  • Checking ReadGroup name in BAM file with GATK instructions
    • Julianne Radford
    • February 16, 2021 19:04
    0 votes 1 comment
  • HaplotypeCaller and Read Group Errors
    • Julianne Radford
    • February 11, 2021 17:45
    0 votes 1 comment
  • HaplotypeCaller -ERC GVCF -variant_index_type LINEAR
    • Matilde
    • January 22, 2021 18:22
    1 vote 1 comment
  • Funcotator missing AF
    • Haiying Kong
    • January 11, 2021 15:13
    0 votes 1 comment
  • MarkDuplicates
    • JAY SINGH
    • January 10, 2021 13:41
    0 votes 1 comment
  • When the useful PGT and PID fields have been implemented in GATK tool for the first time
    • Sandrine lagarrigue
    • December 31, 2020 17:36
    0 votes 1 comment
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