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 comments Newest post Recent activity Votes Comments
  • No results of CollectvariantCallingMetrics Answered
    • Yenan
    • November 30, 2020 07:13
    0 votes 30 comments
  • Genome STRiP CNVDiscovery pipeline error
    • Beilei Bian
    • March 25, 2020 00:39
    0 votes 27 comments
  • ValidateSamFile: New error after running BQSR
    • ISmolicz
    • November 16, 2020 15:21
    0 votes 19 comments
  • How to run GenotypeConcordance
    • Ana Marija
    • September 12, 2020 00:57
    • Edited
    0 votes 19 comments
  • Broken: conda env create -n gatk -f gatkcondaenv.yml
    • James White
    • April 24, 2020 17:01
    0 votes 17 comments
  • Problem Installing GATK python environment - SOLUTION POSTED! Featured
    • SkyWarrior
    • February 06, 2020 07:21
    • Edited
    1 vote 17 comments
  • Panel of Normals Documentation Answered
    • Ryan Gimple
    • April 16, 2020 17:48
    1 vote 16 comments
  • filterSamReads stdout format error
    • rcorbett
    • February 04, 2021 15:31
    • Edited
    0 votes 15 comments
  • ERROR MESSAGE: No gender data for sample:sample7
    • termius
    • August 05, 2020 07:02
    0 votes 15 comments
  • Fatal error occuring during GATK4 PathSeqPipeline tool run
    • Jude Taylor
    • July 14, 2020 12:40
    0 votes 15 comments
  • MarkDuplicatesSparks not removing some duplicates?
    • Tom Morrison
    • June 18, 2020 14:55
    0 votes 15 comments
  • DepthofCoverage GATK4.1.7.0 -gene-list Answered
    • marta r
    • May 27, 2020 14:19
    0 votes 15 comments
  • Setting SPARK resources when using the gatk release version
    • Ury Alon
    • May 18, 2020 04:42
    • Edited
    0 votes 15 comments
  • Genomestrip preprocessing error
    • chae chae
    • March 08, 2022 03:41
    • Edited
    0 votes 13 comments
  • Error running FilterMutectCalls: alpha must be greater than 0 but got NaN
    • Larry S
    • September 20, 2020 14:48
    0 votes 13 comments
  • --tmp-dir option user error Answered
    • Brynjar Sigurðsson
    • August 10, 2020 12:22
    0 votes 13 comments
  • CNNScoreVariants carshes with java.lang.NullPointerException Answered
    • riederd
    • January 17, 2020 15:29
    1 vote 13 comments
  • Any automatic downloadable gatk3?
    • ale
    • January 09, 2020 13:16
    2 votes 13 comments
  • Error in running GenomicsDBConfigException Answered
    • Shivangi Agarwal
    • December 20, 2021 14:51
    0 votes 12 comments
  • mitochondria_m2_wdl: MitochondriaPipeline Issues
    • Valentin
    • July 09, 2020 13:42
    0 votes 12 comments
  • GATK4 HaplotypeCaller ERROR : expected haplotypes.size() >= eventsAtThisLoc.size() + 1
    • Şevval Aktürk
    • April 23, 2020 12:26
    0 votes 12 comments
  • HaplotypeCaller complains (in 2 different ways) about sample-name
    • Terry Jones
    • February 18, 2020 14:07
    0 votes 12 comments
  • Error in SplitNCigarReads
    • Giulia Corsi
    • August 19, 2020 15:26
    0 votes 11 comments
  • Merge different individual VCF
    • Linda Do
    • July 06, 2020 07:05
    1 vote 11 comments
  • FilterByOrientationBias vanished in 4.1.6.0
    • riederd
    • March 30, 2020 11:41
    0 votes 11 comments
  • Does GATK4 BaseRecalibrator not understand relative paths?
    • Eva (Evander)
    • October 17, 2022 12:51
    0 votes 10 comments
  • Error when trying to generate the second recalibration table for AnalyzeCovariates
    • ISmolicz
    • February 17, 2021 12:03
    0 votes 10 comments
  • FixVcfHeader error: A reference dictionary is required for creating Tribble indices on the fly
    • jorgez
    • July 20, 2020 18:52
    0 votes 10 comments
  • LiftoverVcf fails to lift over a GVCF file. Error java.lang.ArrayIndexOutOfBoundsException: -1
    • jorgez
    • May 06, 2020 12:54
    0 votes 10 comments
  • GenomeStrip SVPreprocess works with for a chromosome region; but fail for whole genome Answered
    • APato
    • February 03, 2020 21:28
    0 votes 10 comments
  • 1
  • 2
  • 3
  • 4
  • 5
  • 6
  • ›
  • »

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