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 votes Newest post Recent activity Votes Comments
  • Out of memory error using OpenJDK vs Oracle JDK for CNV-LOH
    • Jose Arcadio Buendia
    • February 28, 2020 01:53
    • Edited
    2 votes 2 comments
  • Known issue: old GATK forum inaccessible Answered
    • Tiffany Miller
    • January 23, 2020 17:47
    • Edited
    2 votes 3 comments
  • Any automatic downloadable gatk3?
    • ale
    • January 09, 2020 13:16
    2 votes 13 comments
  • How do I rename output folder created using glob (WDL-Cromwell)?
    • Mar Quiroga
    • November 25, 2020 23:20
    1 vote 1 comment
  • Where do I find guidance on when to mark duplicates a second time?
    • ISmolicz
    • November 13, 2020 11:54
    1 vote 1 comment
  • VQSR in variants on X chromosome
    • Jaeyoon Chung
    • August 26, 2020 18:27
    1 vote 2 comments
  • Cromwell support for n2 and n2d instance types in GCP
    • Mike Altarace
    • August 06, 2020 01:54
    1 vote 2 comments
  • GenomicsDBImport: Attempting to genotype more than 50 alleles
    • Nils Homer
    • August 06, 2020 00:13
    1 vote 2 comments
  • GenomicsDBImport: has too many genotypes in the combined VCF record
    • Nils Homer
    • August 06, 2020 00:12
    • Edited
    1 vote 2 comments
  • Picard CollectHsMetrics PCT_EXC_OFF_TARGET
    • Holly Corbitt
    • May 07, 2020 04:09
    1 vote 4 comments
  • Problem Installing and testing GATK-4.1.7.0
    • Arjun Upadhaya
    • May 04, 2020 06:34
    1 vote 5 comments
  • Do I need to perform fastqc and adapters trimming before gatk pipeline?
    • LG
    • May 01, 2020 02:49
    1 vote 4 comments
  • jar for mutect 1.1.7
    • Knight Ni
    • April 19, 2020 17:08
    1 vote 6 comments
  • GATK/Picard does not detect mates in paired-end BAM
    • jipvdinter
    • April 07, 2020 11:34
    • Edited
    1 vote 3 comments
  • How do I input two separate paired-end fastq files into the GATK pipeline? Do I use an interleave-fastq?
    • Lauren Fedenia
    • February 21, 2020 20:31
    1 vote 1 comment
  • HaplotypeCaller produces very large .idx files
    • Anze Staric
    • February 20, 2020 20:30
    1 vote 4 comments
  • ValidateSamFile behavior
    • Robert Edgar
    • February 17, 2020 18:07
    1 vote 7 comments
  • Problem Installing GATK python environment - SOLUTION POSTED! Featured
    • SkyWarrior
    • February 06, 2020 07:21
    • Edited
    1 vote 17 comments
  • Typos in docs
    • Andrea Haessly
    • January 29, 2020 20:47
    1 vote 1 comment
  • CNNScoreVariants carshes with java.lang.NullPointerException Answered
    • riederd
    • January 17, 2020 15:29
    1 vote 11 comments
  • GATK Best Practices Mitochondrial Analysis
    • ajwils
    • January 09, 2020 21:15
    • Edited
    1 vote 29 comments
  • MarkDuplicatesSpark crash
    • David Gómez-Sánchez
    • January 07, 2020 17:02
    1 vote 9 comments
  • BaseRecalibrator on MT .bam files
    • Sharon Cox
    • February 19, 2021 09:48
    • Edited
    0 votes 1 comment
  • LiftoverVcf: hg19 to hg38 all variants mismatched
    • Ken Hanscombe
    • February 17, 2021 14:13
    0 votes 3 comments
  • Error when trying to generate the second recalibration table for AnalyzeCovariates
    • ISmolicz
    • February 17, 2021 12:03
    0 votes 9 comments
  • Checking ReadGroup name in BAM file with GATK instructions
    • Julianne Radford
    • February 16, 2021 19:04
    0 votes 1 comment
  • How to work with CNN variant caller
    • Danio Rerio
    • February 16, 2021 16:09
    0 votes 3 comments
  • Mitochondrial analysis - FilterMutectCalls autosomal-coverage is not an option
    • leory
    • February 16, 2021 13:42
    0 votes 1 comment
  • HaplotypeCaller and Read Group Errors
    • Julianne Radford
    • February 11, 2021 17:45
    0 votes 1 comment
  • DepthOfCoverage Error: Refseq file contains transcripts with zero coding length
    • ashgorden
    • February 04, 2021 08:15
    0 votes 2 comments
  • 1
  • 2
  • 3
  • 4
  • 5
  • 6
  • ›
  • »

Welcome

GATK Announcements

Read Before You Post

How to Write a 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