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. Documentation Questions

Documentation Questions

Follow New posts New posts and comments

Show all All Planned Not planned Completed Answered No status Sort by recent activity Newest post Recent activity Votes Comments
  • GATK GenotypeGVCFs miss a real Insertion Answered
    • touyupang
    • February 18, 2022 07:45
    0 votes 6 comments
  • germline-resource Answered
    • Juechen Yang
    • March 17, 2020 17:32
    0 votes 10 comments
  • Mosaic gCNVs with GATK Answered
    • Naga
    • January 13, 2022 17:32
    • Edited
    0 votes 1 comment
  • WDL pipeline: Mitochondrial-short-variant-discovery Answered
    • manolis
    • January 25, 2022 07:57
    0 votes 2 comments
  • GenomicsDBImport -L [string] (but for the whole genome): purpose to generate invariant sites Answered
    • Pete Thorpe
    • January 20, 2022 08:51
    0 votes 8 comments
  • stand_call_conf and stand_emit_conf in GATK 4.2.4.1 Answered
    • M.R-E.H
    • January 17, 2022 16:05
    0 votes 1 comment
  • "main" java.lang.OutOfMemoryError: Requested array size exceeds VM limit Answered
    • 蒲鹏
    • January 12, 2022 10:12
    0 votes 4 comments
  • CollectReadCounts tutorial incorrectly states default read quality threshold Answered
    • simon lee
    • December 14, 2021 04:06
    • Edited
    0 votes 1 comment
  • Ploidy as an argument in Mutect2 Answered
    • Michael Weinstein
    • May 21, 2021 00:46
    0 votes 5 comments
  • "NotDuplicateReadFilter" behaviour in HaplotypeCaller Answered
    • sanjeevksh
    • December 07, 2021 21:40
    0 votes 3 comments
  • picard sortvcf: what does it do? Answered
    • Thomas Juettemann
    • November 09, 2021 17:31
    0 votes 7 comments
  • Unable to find full Best Practices workflow for short variant joint genotyping
    • Kirsten Dimmler
    • November 23, 2021 17:41
    0 votes 1 comment
  • What's wrong with my GATK HaplotypeCaller step's codes?
    • Han Li
    • November 29, 2021 05:18
    0 votes 1 comment
  • Append GenomicsDBimport Answered
    • wbsimey
    • November 18, 2021 18:26
    • Edited
    0 votes 3 comments
  • How can I get Sample Summary
    • rq m
    • November 19, 2021 08:10
    • Edited
    0 votes 1 comment
  • GATK Best Practices Mitochondrial Analysis Answered
    • ajwils
    • January 09, 2020 21:15
    • Edited
    1 vote 45 comments
  • GATK4.2.3.0 HaplotypeCaller error
    • Alicia
    • November 13, 2021 12:49
    0 votes 1 comment
  • BQSR: Do read filters used by BQSR tools need to be applied to data prior to assessing the number of bases per read group? Answered
    • ISmolicz
    • November 17, 2020 17:02
    0 votes 2 comments
  • FilterFuncotations Duplicate key error Answered
    • Azza Ahmed
    • October 14, 2021 10:53
    0 votes 7 comments
  • Where do I find guidance on when to mark duplicates a second time? Answered
    • ISmolicz
    • November 13, 2020 11:54
    1 vote 2 comments
  • --dbsnp option in HaplotypeCaller and other programs Answered
    • gwotto
    • July 01, 2021 12:21
    0 votes 3 comments
  • haplotypeCaller phasing Answered
    • Jeremie Kalfon
    • October 05, 2021 15:07
    • Edited
    0 votes 11 comments
  • `FilterMutectCalls` for normal only calls Answered
    • AMN
    • September 10, 2021 16:17
    • Edited
    0 votes 4 comments
  • How does Genomicsdbimport for polyploids work?
    • Homa Papoli
    • October 25, 2021 08:57
    0 votes 2 comments
  • VariantsToTable GT not extracting correctly Answered
    • Asha Mehta
    • October 15, 2021 19:59
    • Edited
    0 votes 1 comment
  • Difference between the different annotation groups available in GATK
    • Shashank Nagaraja
    • October 04, 2021 22:15
    2 votes 1 comment
  • GATK VariantFiltration Error Answered
    • Reza
    • September 05, 2021 07:48
    0 votes 3 comments
  • use LearnReadOrientationModel to build artifact-prior.tar.gz Answered
    • chenglei
    • September 22, 2021 14:48
    0 votes 5 comments
  • How do I call somatic mitochondrial variants? Answered
    • Ruiqiao Bai
    • September 14, 2021 04:03
    0 votes 3 comments
  • Interpretation of gene_summary output from DepthofCoverage Answered
    • neethukrishna Kausthubham
    • August 26, 2021 11:08
    0 votes 11 comments
  • «
  • ‹
  • 1
  • 2
  • 3
  • 4
  • 5
  • 6
  • 7
  • 8
  • ›
  • »

Welcome

Forum Guidelines

GATK Announcements

Become a GATK Guru

Read Before You Post

Get Email Notifications

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