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 answered All Planned Not planned Completed Answered No status Sort by recent activity Newest post Recent activity Votes Comments
  • Why don't I have access to some links? Answered
    • Manuel
    • January 12, 2022 11:13
    0 votes 3 comments
  • GATK Mutect2 tumor vs. normal sample Answered
    • Enrico Cocchi
    • October 02, 2020 16:23
    0 votes 4 comments
  • vcf files for BQSR step Answered
    • Varun Gupta
    • March 30, 2020 22:13
    1 vote 4 comments
  • mutect2 multi-sample Answered
    • zhao shilin
    • May 07, 2020 17:27
    • Edited
    0 votes 35 comments
  • Picard SortSam error Answered
    • Tanay Biswas
    • October 14, 2022 11:18
    0 votes 3 comments
  • Issues with LiftoverVcf Answered
    • Mohammad Deen Hayatu
    • October 06, 2022 06:43
    0 votes 6 comments
  • SamToFastq - bam order Answered
    • Jakub Savara
    • July 24, 2022 10:48
    0 votes 6 comments
  • HaplotypeCaller using one sample split in two bam files Answered
    • elena vigorito
    • June 28, 2022 09:16
    0 votes 3 comments
  • ASEReadCount Only Outputting the First Chromosome Answered
    • Leslie Youtsey
    • August 31, 2022 19:31
    0 votes 3 comments
  • Too many duplicate articles Answered
    • Дмитрий Голик
    • September 09, 2022 09:14
    0 votes 2 comments
  • Where is the list of annotations and annotation groups? Answered
    • tedtoal
    • July 05, 2021 23:05
    2 votes 7 comments
  • germline mutation calling using per-sample module Answered
    • chenglei
    • June 08, 2022 16:06
    0 votes 2 comments
  • ASEReadCounter outputting blank table Answered
    • Leslie Youtsey
    • August 24, 2022 17:53
    • Edited
    0 votes 4 comments
  • GATK CNV somatic panels of normal design Answered
    • Mallika Gandham
    • May 04, 2022 16:07
    0 votes 3 comments
  • Mitochondrial shifted reference Answered
    • MARC TORMO PUIGGROS
    • January 26, 2022 10:57
    0 votes 4 comments
  • Limit core use of DetermineGermlineContigPloidy & GermlineCNVCaller Answered
    • Blaz Vrhovsek
    • June 30, 2022 11:27
    1 vote 1 comment
  • GATK genomicsDBImport error Answered
    • @OK
    • June 14, 2022 11:11
    0 votes 3 comments
  • Documentation for running GATK and Cromwell on IBM Cloud Answered
    • Takeshi Yoshimura
    • April 05, 2022 01:24
    1 vote 7 comments
  • Haplotypecaller Answered
    • Mahdi Ahmadi
    • May 30, 2022 16:45
    0 votes 1 comment
  • JointGermlineCNVSegmentation Answered
    • Yangyxt
    • April 30, 2022 06:56
    0 votes 2 comments
  • BaseRecalibrator --max-cycle Answered
    • oğuzhan karaosmanoğlu
    • May 12, 2022 11:11
    0 votes 1 comment
  • Question on Java version Answered
    • Anand
    • May 10, 2022 15:24
    0 votes 2 comments
  • GetPileupSummaries common germline variant sites VCF hg38 Answered
    • Anish K
    • April 18, 2022 16:48
    0 votes 2 comments
  • MergeBamAlignment for mitochondrial variant discovery Answered
    • Ahmed S. Chakroun
    • March 18, 2022 17:33
    0 votes 1 comment
  • how to run "gatk-register"? Answered
    • Mahendra Singh
    • March 28, 2022 04:28
    0 votes 2 comments
  • MergeBamAlignment conflicting headers between mapped and unmapped Answered
    • TA
    • March 04, 2022 15:13
    0 votes 3 comments
  • Is FilterAlignmentArtifacts out of the Mutect2 calling best practices? Answered
    • shenglai
    • March 11, 2022 01:53
    0 votes 1 comment
  • genotyping calls don't align with coverage Answered
    • Gertjan Wils
    • March 15, 2022 12:57
    1 vote 1 comment
  • How is tumor_f in Funcotator MAF Answered
    • Robert Bremel
    • May 26, 2020 17:11
    0 votes 3 comments
  • VariantsToTable not working Answered
    • Arwa Ahmad
    • February 25, 2022 08:56
    0 votes 2 comments
  • 1
  • 2
  • 3
  • 4
  • 5
  • ›
  • »

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