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 comments Newest post Recent activity Votes Comments
  • GenotypeGVCFs stalls while using --all-sites
    • Rachael Bay
    • September 15, 2020 22:13
    0 votes 18 comments
  • GenomicsDBImport very slow on genome with many contigs
    • Marley Yeong
    • April 02, 2020 15:22
    1 vote 13 comments
  • Provider "genedb" not found when using SelectVariants & GenomicsDBImport
    • Lucas Carey
    • March 12, 2020 02:00
    0 votes 11 comments
  • GenomicsDBimport not importing all the batches
    • Vinod Kumar
    • January 20, 2021 14:56
    • Edited
    0 votes 10 comments
  • Getting an error with genomicsdbimport
    • Vinod Kumar
    • November 09, 2020 16:35
    • Edited
    0 votes 9 comments
  • HaplotypeCaller too many alternative alleles found
    • madzayasodara
    • July 15, 2020 19:10
    0 votes 9 comments
  • Unphased homozyous sites between phased heterozygous sites
    • OzAy
    • January 14, 2020 19:39
    • Edited
    0 votes 9 comments
  • ApplyBQSR to unmapped reads for non-model organism does not work with '-L unmapped' flag
    • cali
    • September 02, 2020 23:17
    0 votes 8 comments
  • GenotypeGvcfs has formatting issues in both v4.1.6.0 as v4.1.7.0
    • ABours
    • May 29, 2020 18:23
    0 votes 8 comments
  • HaplotypeCaller local Assembly
    • Etergemina
    • April 21, 2020 09:37
    • Edited
    0 votes 8 comments
  • Empty vcf after GenotypeVCFs when combining already genotyped samples
    • leze
    • April 08, 2020 22:40
    0 votes 8 comments
  • Error running HaplotypeCaller?
    • vctrymao
    • January 08, 2020 15:42
    0 votes 8 comments
  • emit-ref-confidence error
    • Florence Morel
    • December 28, 2020 17:38
    0 votes 7 comments
  • FixMateInformation does not solve ERROR:MATE_NOT_FOUND
    • Simon Hellemans
    • November 14, 2020 07:09
    • Edited
    1 vote 7 comments
  • Missing MQ scores in gvcf
    • Heather Tuttle
    • October 26, 2020 22:22
    0 votes 7 comments
  • HaplotypeCaller for haploid genome
    • Pummi Singh
    • September 06, 2020 23:30
    0 votes 7 comments
  • Which exact info does BaseRecalibrator uses from a vcf?
    • madzayasodara
    • August 12, 2020 00:28
    0 votes 7 comments
  • Alignment file does not exist: 08.strip/metadata/headers.bam when running GenomeStrip SVPreprocess
    • Jinpeng Wang
    • July 31, 2020 10:37
    • Edited
    0 votes 7 comments
  • About Bam file input problem in HaplotypCaller
    • 酒香彈箏
    • February 03, 2021 08:42
    • Edited
    0 votes 6 comments
  • haplotypecallerspark wants DS_Store
    • John Denton
    • January 14, 2021 14:53
    0 votes 6 comments
  • Haplotype caller error; java.lang.IllegalStateException: Graph must have ref source and sink vertices
    • New_gatk_user
    • August 11, 2020 15:12
    0 votes 6 comments
  • A USER ERROR has occurred: Badly formed genome unclippedLoc: Parameters to GenomeLocParser are incorrect:The stop position 0 is less than start 1 in contig contig004333
    • New_gatk_user
    • August 04, 2020 11:43
    • Edited
    0 votes 6 comments
  • GATK4 - Parallelizing genotypegvcfs
    • Pietro Mello
    • April 01, 2020 22:17
    0 votes 6 comments
  • "No positional argument is defined" Error in HaplotypeCaller
    • Julianne Radford
    • February 06, 2021 21:07
    0 votes 5 comments
  • Missing samples from the output vcf file produced with GenotypeGVCFs
    • Patrícia H. Brito
    • January 08, 2021 11:41
    0 votes 5 comments
  • Missing value evaluate as fail
    • Laura
    • August 14, 2020 00:16
    0 votes 5 comments
  • Cannot run through CNVDiscoverypipeline
    • Jinpeng Wang
    • August 08, 2020 14:55
    0 votes 5 comments
  • How to filter on SnpEff EFF field using GATK
    • Aditi Batra
    • July 17, 2020 17:14
    0 votes 5 comments
  • SNP calling with multi-sample plant data
    • Sin Lee
    • May 14, 2020 02:37
    0 votes 5 comments
  • Fungal mitochondrial variant calling
    • Yue Wang
    • May 07, 2020 18:48
    • Edited
    0 votes 5 comments
  • 1
  • 2
  • 3
  • 4
  • 5
  • ›
  • »

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