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 comments Newest post Recent activity Votes Comments
  • humanG1Kv37 to hg38 liftover issues
    • brian miller
    • June 06, 2020 00:44
    • Edited
    0 votes 3 comments
  • CombineGVCF slowing down at certain region on chromosome 1
    • wd
    • May 26, 2020 18:38
    • Edited
    0 votes 3 comments
  • HaplotypeCaller on multiple BAMs vs Joint-Call Cohort
    • lahl
    • May 12, 2020 20:21
    0 votes 3 comments
  • Output vcf file from HaplotypeCaller mostlly contain <NON_REF> alteration
    • Jay Singh
    • May 12, 2020 14:58
    0 votes 3 comments
  • CombineGVCFs Fails for a batch of 2 samples where samples shows high number of alternate INDEL Alleles
    • info 2020
    • April 29, 2020 20:24
    0 votes 3 comments
  • Cromwell GATK json list of files
    • Kristian Unger
    • April 16, 2020 07:41
    0 votes 3 comments
  • Mutect2-exome-panel.vcf Not Found
    • Ryan Gimple
    • April 11, 2020 20:03
    0 votes 3 comments
  • multiple vcf files in FastaAlternateReferenceMaker
    • mk
    • April 09, 2020 04:59
    0 votes 3 comments
  • VariantFiltration Invalid Argument
    • mons7re
    • April 08, 2020 10:57
    0 votes 3 comments
  • GATK/Picard does not detect mates in paired-end BAM
    • jipvdinter
    • April 07, 2020 11:34
    • Edited
    1 vote 3 comments
  • GenotypeGVCFs: unexpected output in PGT and PID fields
    • Johnny Li
    • March 31, 2020 21:35
    • Edited
    0 votes 3 comments
  • Error using a edited gatk wdl (bam-unmapped-bam workflow) to accept array[files] as input rather than a single .bam file
    • sahuno
    • March 28, 2020 19:11
    0 votes 3 comments
  • Getting CNNScoreVariants to run faster
    • WVNicholson
    • March 18, 2020 16:29
    0 votes 3 comments
  • Why does my vcf contain a genotype when there are no reads supporting it?
    • Jeff Duty
    • February 27, 2020 14:51
    • Edited
    0 votes 3 comments
  • What kind of statistical methods genome strip used?
    • zhangwusheng
    • February 19, 2020 18:21
    0 votes 3 comments
  • What is the 'physical phasing'
    • whynot
    • February 13, 2020 04:29
    0 votes 3 comments
  • Where's the DRAGEN?
    • Matthias De Smet
    • February 11, 2020 08:29
    0 votes 3 comments
  • GATK Workshop Registration Details
    • margherita mutarelli
    • January 29, 2020 11:39
    0 votes 3 comments
  • Known issue: old GATK forum inaccessible Answered
    • Tiffany Miller
    • January 23, 2020 17:47
    • Edited
    2 votes 3 comments
  • Genomestrip: Argument with name '--ploidyMapFile' (-ploidyMapFile) is missing
    • Senwei
    • April 27, 2022 07:59
    1 vote 2 comments
  • change the memory when running SVPreprocess
    • zzq
    • January 11, 2022 06:21
    • Edited
    0 votes 2 comments
  • Funcotator gnomAD MAF columns Answered
    • TMB
    • August 23, 2021 02:04
    0 votes 2 comments
  • Docker image for GATK3 version 3.7 Answered
    • Tatyana Zhuravleva
    • June 27, 2021 01:29
    0 votes 2 comments
  • Picard liftover Issue bostau8 to bostau6 Answered
    • Abrish
    • May 31, 2021 10:20
    0 votes 2 comments
  • DepthOfCoverage Error: Refseq file contains transcripts with zero coding length
    • ashgorden
    • February 04, 2021 08:15
    0 votes 2 comments
  • Reference Fasta vs Alt Reference Fasta
    • Linda Do
    • January 29, 2021 21:56
    0 votes 2 comments
  • Mutect2: NuMTs filtering on RNA-seq Answered
    • Leore Nehemie Bensabath
    • January 29, 2021 15:57
    0 votes 2 comments
  • Resource bundle for GRCh37
    • Reda
    • January 17, 2021 17:38
    0 votes 2 comments
  • Any documents for 199 columns in Funcotator output?
    • Haiying Kong
    • January 07, 2021 10:03
    0 votes 2 comments
  • GenomicsDBImport: can different VCF files be imported into one genomicsdb workspace against different interval lists?
    • ISmolicz
    • December 02, 2020 17:43
    0 votes 2 comments
  • «
  • ‹
  • 1
  • 2
  • 3
  • 4
  • 5
  • 6
  • 7
  • 8
  • 9
  • 10
  • ›
  • »

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