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 no status All Planned Not planned Completed Answered No status Sort by recent activity Newest post Recent activity Votes Comments
  • Genotype filtering still write "PASS" in filter field
    • Marissa Eronika
    • March 21, 2023 15:50
    1 vote 3 comments
  • is --dont-use-soft-clipped-bases discarded in HaplotypeCaller?
    • Songming Liu
    • March 24, 2023 07:45
    0 votes 1 comment
  • Why is the coverage cut abruptly for a region in the bamout file of Mutect2 in comparison to the region in input files?
    • ISmolicz
    • March 21, 2023 00:15
    0 votes 1 comment
  • Using haplotype information from high-coverage samples as a prior for Haplotypecaller for other low-coverage samples in the same dataset?
    • Nils Paffen
    • March 07, 2023 16:43
    0 votes 1 comment
  • Intervals and GenomicsDBImport
    • Irbin Manuel Veliz Isidro
    • February 17, 2023 09:35
    0 votes 2 comments
  • Picard CollectHsMetrics PCT_TARGET_BASES Output
    • michaelmc
    • February 23, 2023 17:04
    0 votes 2 comments
  • Funcotator 4.1.2.0 gencode for locatableXSV
    • Frank Maiwald
    • February 20, 2023 11:55
    0 votes 1 comment
  • error:Argument --emit-ref-confidence
    • Rezwan Tariq
    • February 22, 2023 10:09
    0 votes 0 comments
  • gatk SelectVariant identified no snps in the vsf file while it has 63702926 snps
    • Vishal Negi
    • February 06, 2023 19:24
    0 votes 1 comment
  • Variables harmonization tutorial for variables collected from Pic-sure from various cohort
    • kei_hang_chan
    • January 26, 2023 06:18
    0 votes 0 comments
  • Picard's CollectRnaSeqMetrics
    • Benli Chai
    • January 17, 2023 20:36
    0 votes 0 comments
  • Detailed reason for filtering by FilterMutectCalls
    • tan qiang
    • January 13, 2023 07:44
    0 votes 0 comments
  • How to specify number of threads while running Mutect2
    • Tanay Biswas
    • December 21, 2022 05:49
    0 votes 0 comments
  • Should we run MarkDuplicates on PCR-Free Libraries made using PCR-Free Kits to take care of Optical Duplicates ?
    • rohit satyam
    • July 28, 2020 20:28
    • Edited
    0 votes 3 comments
  • BuildBamIndex
    • Robert Bremel
    • November 08, 2022 20:27
    0 votes 4 comments
  • Best practice trios
    • Sheryl
    • November 23, 2022 00:58
    • Edited
    0 votes 0 comments
  • Java exception: index 65 is CONSTANT_MethodRef and should be CONSTANT_InterfaceMethodRef
    • Julián García-Abadillo
    • October 27, 2022 13:37
    • Edited
    0 votes 2 comments
  • What does RAW_MQ annotation mean ?
    • Robert Baldwin
    • July 27, 2022 19:49
    0 votes 3 comments
  • Can't access google cloud it says permission required
    • HQ Zhao
    • October 27, 2022 02:03
    0 votes 2 comments
  • Report file CreateExtendedIlluminaManifest Report file
    • James Gallant
    • October 31, 2022 15:28
    1 vote 1 comment
  • RGID versus RGPU
    • Jean-Michel Carter
    • October 20, 2022 06:49
    • Edited
    0 votes 1 comment
  • Picard CollectHsMetrics output
    • Giovanni Cerchia
    • July 21, 2022 12:29
    0 votes 3 comments
  • Mutect2 produces 0 results for somatic mutation calling of paired-end reads (BAM)
    • Di Pan
    • October 09, 2022 05:22
    • Edited
    0 votes 1 comment
  • UmiAwareMarkDuplicatesWithMateCigar - UMI_METRICS
    • Miguel Grau
    • September 13, 2022 10:55
    • Edited
    0 votes 2 comments
  • Documentation for interval files in resource bundle
    • Laura Egolf
    • September 19, 2022 21:28
    0 votes 1 comment
  • CalculateFingerprintMetrics Usability On Somatic Samples
    • Kathryn Kananen
    • September 13, 2022 04:16
    • Edited
    0 votes 1 comment
  • Request: examples of svtk usage
    • Yaping Wu
    • September 10, 2022 01:30
    0 votes 1 comment
  • GenomicsDBImport function is not executing: Aborted (core dumped)
    • Tanay Biswas
    • August 22, 2022 11:23
    0 votes 2 comments
  • Calculating FQ or an FQ-like score from information in GATK4 vcf
    • Tris O'Brien Dodge
    • August 31, 2022 09:15
    0 votes 1 comment
  • How to use Funcotator for PostprocessGermlineCNVCalls results
    • jiaren zhang
    • August 22, 2022 01:42
    0 votes 1 comment
  • 1
  • 2
  • 3
  • ›
  • »

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