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. Non-Human

Non-Human

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
  • REAL Variant not called by HaplotypeCaller Answered
    • HASSAN BADRANE
    • December 15, 2020 23:45
    1 vote 4 comments
  • FixMateInformation does not solve ERROR:MATE_NOT_FOUND
    • Simon Hellemans
    • November 14, 2020 07:09
    • Edited
    1 vote 7 comments
  • GATK-HaplotypeCaller results generate records with read depth of zero?
    • xie186
    • June 25, 2020 14:08
    1 vote 2 comments
  • HaplotypeCaller for denovo RNAseq output
    • krunal pawar
    • May 09, 2020 11:50
    1 vote 3 comments
  • GenomicsDBImport very slow on genome with many contigs Answered
    • Marley Yeong
    • April 02, 2020 15:22
    1 vote 17 comments
  • Analy
    • Thomaz Marques Sena
    • March 25, 2020 19:58
    1 vote 3 comments
  • HaplotypeCaller does not recognize the RefSeqfile
    • Newcomer
    • March 18, 2020 09:18
    1 vote 2 comments
  • GATK for Rnor6 - Funcotator error
    • Ngoc Khoi Dang
    • August 03, 2022 16:30
    • Edited
    0 votes 0 comments
  • java.lang.IllegalStateException in GenotypeGVCFs after GenomicsDBImport, GATK 4.2.6.1 Answered
    • Zane Swaydan
    • June 30, 2022 11:38
    • Edited
    0 votes 8 comments
  • All intervals were filtered in Filterintervals
    • 侯旻
    • May 31, 2022 08:24
    0 votes 11 comments
  • FindBreakpointEvidenceSpark sudden shutdown Answered
    • Domniki Manousi
    • March 07, 2022 12:01
    0 votes 4 comments
  • emit-ref-confidence error Answered
    • Camila Martínez Avila
    • February 08, 2022 00:44
    0 votes 3 comments
  • gatk4-4.2.4.0-0 Fixmate Error Answered
    • Abrish
    • January 26, 2022 10:25
    • Edited
    0 votes 2 comments
  • GATK HaplotypeCaller disable filter -DF with the error in positional argument value Answered
    • Frans Dany
    • January 14, 2022 03:00
    0 votes 1 comment
  • VariantEval does not work or something wrong with my ref genome and dbsnps? Answered
    • Anh Mai
    • January 04, 2022 10:45
    0 votes 5 comments
  • ValidateSamFile Error Answered
    • Abrish
    • January 04, 2022 14:11
    • Edited
    0 votes 1 comment
  • Query regarding CombineGVCFs Answered
    • Abrish
    • December 20, 2021 17:54
    0 votes 4 comments
  • Inconsistent variant call in some pool-seq samples Answered
    • Lorena
    • December 10, 2021 15:53
    0 votes 3 comments
  • Selectvariants for SNPs selection produces .vcf file without homozygous-REF calls
    • Amod Kumar
    • December 02, 2021 11:03
    0 votes 5 comments
  • GatherVcfs - File number limit?
    • rokkineste
    • November 22, 2021 12:14
    • Edited
    0 votes 3 comments
  • GATK GenotypeGVCFs stuck on starting traversal Answered
    • Mary Happ
    • November 11, 2021 19:38
    • Edited
    0 votes 7 comments
  • How do iquery VCF for specific variants by CHROM and POS
    • Alon Ziv
    • October 30, 2021 09:40
    0 votes 3 comments
  • No downsampling with max-reads-per-alignment-start
    • Liang Ye
    • October 28, 2021 01:37
    • Edited
    0 votes 3 comments
  • ArtificialHaplotypeRG makes variant heterozygous Answered
    • Wiebe Kooistra
    • September 29, 2021 14:34
    0 votes 5 comments
  • GenomicsDBimport and CombineGVCF does not show variants at ~500 Mbp onwards, although gvcf files from HapolypeCaller report variants
    • Hanin
    • September 27, 2021 07:22
    • Edited
    0 votes 5 comments
  • is it ok to apply BQSR and HaplotypeCaller to autosome noncoding region by -L by chromoosme?
    • Shanshan
    • September 09, 2021 02:44
    0 votes 2 comments
  • Preform variant calling on 50 bp SE rna-seq data
    • Alon Ziv
    • September 03, 2021 05:35
    0 votes 4 comments
  • gatk MarkDuplicatesSpark exits without error message Answered
    • Ramesh Ramasamy
    • July 22, 2021 01:15
    • Edited
    0 votes 3 comments
  • HaplotypeCaller with additional annotation? Answered
    • Sarah Bonnin
    • June 30, 2021 13:06
    0 votes 5 comments
  • Issues while running GenotypeGVCFs Answered
    • sanjeevksh
    • June 25, 2021 04:16
    • Edited
    0 votes 11 comments
  • 1
  • 2
  • 3
  • 4
  • 5
  • ›
  • »

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