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 newest post Newest post Recent activity Votes Comments
  • Why don't I have access to some links? Answered
    • Manuel
    • January 12, 2022 11:13
    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
  • "NotDuplicateReadFilter" behaviour in HaplotypeCaller Answered
    • sanjeevksh
    • December 07, 2021 21:40
    0 votes 3 comments
  • What's wrong with my GATK HaplotypeCaller step's codes?
    • Han Li
    • November 29, 2021 05:18
    0 votes 1 comment
  • Unable to find full Best Practices workflow for short variant joint genotyping
    • Kirsten Dimmler
    • November 23, 2021 17:41
    0 votes 1 comment
  • How can I get Sample Summary
    • rq m
    • November 19, 2021 08:10
    • Edited
    0 votes 1 comment
  • Append GenomicsDBimport Answered
    • wbsimey
    • November 18, 2021 18:26
    • Edited
    0 votes 3 comments
  • GATK4.2.3.0 HaplotypeCaller error
    • Alicia
    • November 13, 2021 12:49
    0 votes 1 comment
  • picard sortvcf: what does it do? Answered
    • Thomas Juettemann
    • November 09, 2021 17:31
    0 votes 7 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
  • FilterFuncotations Duplicate key error Answered
    • Azza Ahmed
    • October 14, 2021 10:53
    0 votes 7 comments
  • haplotypeCaller phasing Answered
    • Jeremie Kalfon
    • October 05, 2021 15:07
    • Edited
    0 votes 11 comments
  • Difference between the different annotation groups available in GATK
    • Shashank Nagaraja
    • October 04, 2021 22:15
    2 votes 1 comment
  • use LearnReadOrientationModel to build artifact-prior.tar.gz Answered
    • chenglei
    • September 22, 2021 14:48
    0 votes 5 comments
  • Mark duplicates in merged bam files sorted by coordinates
    • Priyadarshini Thirunavukkarasu
    • September 14, 2021 08:16
    0 votes 2 comments
  • How do I call somatic mitochondrial variants? Answered
    • Ruiqiao Bai
    • September 14, 2021 04:03
    0 votes 3 comments
  • `FilterMutectCalls` for normal only calls Answered
    • AMN
    • September 10, 2021 16:17
    • Edited
    0 votes 4 comments
  • countsN meaning & example Answered
    • Mingzhou Fu
    • September 08, 2021 15:38
    0 votes 2 comments
  • GATK VariantFiltration Error Answered
    • Reza
    • September 05, 2021 07:48
    0 votes 3 comments
  • How does GATK HaplotypeCaller behave with respect to deletions that span across a supplied interval in a bed file using -L? Answered
    • Rachel Duffin
    • August 27, 2021 11:02
    0 votes 3 comments
  • SelectVariants --discordance not working as I expected Answered
    • Carlos P Arques
    • August 26, 2021 21:10
    • Edited
    0 votes 3 comments
  • Interpretation of gene_summary output from DepthofCoverage Answered
    • neethukrishna Kausthubham
    • August 26, 2021 11:08
    0 votes 11 comments
  • JEXL expression for filtering on AD (SelectVariants / FastaAlternateReferenceMaker)
    • Yanis Chrys
    • August 19, 2021 11:35
    0 votes 4 comments
  • GenotypeGVCFs only accepts single combinedGVCF? CombineGVCFs & genomicsdb errors... .interval_list subset Answered
    • Mingzhou Fu
    • July 29, 2021 22:42
    0 votes 12 comments
  • Where do I find resources for using FilterVariantTranches with CNN_2D/CNN_1D scores? Answered
    • Rodrigo Cabrera
    • July 29, 2021 20:00
    0 votes 1 comment
  • Does CollectReadCounts Count Fragments or Individual Reads? Answered
    • Fong Chun Chan
    • July 16, 2021 09:19
    • Edited
    0 votes 3 comments
  • MarkDuplicates not checking sequences Answered
    • Naomie Abecassis
    • July 13, 2021 13:35
    0 votes 3 comments
  • Where is the list of annotations and annotation groups? Answered
    • tedtoal
    • July 05, 2021 23:05
    1 vote 6 comments
  • «
  • ‹
  • 1
  • 2
  • 3
  • 4
  • 5
  • 6
  • ›
  • »

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