Logo
User Guide Tool Index Blog Forum DRAGEN-GATK Events Download GATK4
Sign in

Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

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

  1. GATK
  2. Community
  3. Other

Other

Follow New posts New posts and comments

Show all All Planned Not planned Completed Answered No status Sort by newest post Newest post Recent activity Votes Comments
  • How to run muTect without normal sample? Answered
    • Yingjie Zhu
    • July 11, 2022 21:35
    1 vote 3 comments
  • Accessing the resource bundle. Answered
    • nagam surya
    • June 28, 2022 18:35
    0 votes 6 comments
  • 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
  • Genomestrip: Argument with name '--ploidyMapFile' (-ploidyMapFile) is missing
    • Senwei
    • April 27, 2022 07:59
    1 vote 2 comments
  • Refseq accession number and version number in Funcotator Answered
    • TMB
    • April 26, 2022 04:13
    0 votes 4 comments
  • CNNScoreVariants Issues with environment and Java version Answered
    • Kathrin B
    • April 13, 2022 15:07
    • Edited
    0 votes 6 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
  • Local WDL Mitochondria Pipeline - Import failed Answered
    • Michael
    • March 08, 2022 09:25
    • Edited
    0 votes 1 comment
  • Genomestrip preprocessing error
    • chae chae
    • March 08, 2022 03:41
    • Edited
    0 votes 13 comments
  • Error in GenomicsDBImport: Invalid deflate block found Answered
    • Lauren Hennelly
    • February 26, 2022 20:26
    1 vote 6 comments
  • GC overhead limit exceeded using Mutect2 only tumor version Answered
    • Shirliya Dadon
    • February 09, 2022 12:53
    • Edited
    0 votes 5 comments
  • GATK R plots with R v4.1.2 Answered
    • Franz Gassner
    • January 24, 2022 09:36
    0 votes 3 comments
  • change the memory when running SVPreprocess
    • zzq
    • January 11, 2022 06:21
    • Edited
    0 votes 2 comments
  • Error in running GenomicsDBConfigException Answered
    • Shivangi Agarwal
    • December 20, 2021 14:51
    0 votes 12 comments
  • VariantsToTable positional argument eror
    • Owen Hudson
    • December 14, 2021 17:22
    0 votes 1 comment
  • CollectRnaSeqMetrics GL000220 test not counting ribosomal reads Answered
    • rcorbett
    • December 06, 2021 18:45
    0 votes 5 comments
  • MarkduplicatesSpark failed Answered
    • lid.zigh
    • November 23, 2021 13:44
    0 votes 5 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
  • CalculateContamination 4.1.2.0 org.apache.commons.math3.exception.TooManyEvaluationsException
    • 陈星瀚
    • October 29, 2021 09:21
    0 votes 1 comment
  • Contamination calculation on single file don't detect contaminated samples Answered
    • Vladislav Maximov
    • October 14, 2021 15:03
    0 votes 7 comments
  • GenomincsDBImport Failed to create reader from file: An index is required, but none found., for input source: Answered
    • Morgan Sparks
    • October 12, 2021 11:46
    0 votes 6 comments
  • markduplicatesSpark .bam.parts output error (directory already exists) Answered
    • Morgan Sparks
    • September 30, 2021 16:31
    0 votes 3 comments
  • HaplotypeCaller inconsistency with different interval lists
    • Gytis Mackevičius
    • September 10, 2021 05:53
    • Edited
    0 votes 5 comments
  • My recalibration table from BaseRecalibrator is empty
    • Calum Tattersfield
    • August 25, 2021 18:14
    • Edited
    0 votes 5 comments
  • Funcotator gnomAD MAF columns Answered
    • TMB
    • August 23, 2021 02:04
    0 votes 2 comments
  • Can't explain the number of reads FilterSamReads outputs Answered
    • Aki Jarl Laruson
    • July 28, 2021 23:29
    0 votes 8 comments
  • «
  • ‹
  • 1
  • 2
  • 3
  • 4
  • 5
  • 6
  • 7
  • ›
  • »

Welcome

Forum Guidelines

GATK Announcements

Become a GATK Guru

Read Before You Post

Get Email Notifications

GATK Team Out of Office

The GATK team will be out of office during December 9th 2022 to January 9th 2022 in observance of the holidays. We will not be able to answer posts from within this period. If you are still experiencing issues when we are back, please re-post your inquiry.

Didn't find what you were looking for?

New post

Quick Links

GATK Latest Releases

Known Issues & Troubleshooting

Submitting a Bug Report

How to Track a Github issue

GATK on the Cloud with Terra

Recent GATK News

GATK Blog Posts

GATK Twitter Page

About the GATK community

  • 133,119 Total Users
  • 0 Comments
  • 0 Posts
  • 0 Votes

footer-logo © Broad Institute

  • twitter icon
  • facebook icon
  • linkedin icon
Powered by Zendesk