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 no status All Planned Not planned Completed Answered No status Sort by newest post Newest post Recent activity Votes Comments
  • CombineGVCFs with error output
    • Yifei Sun
    • September 27, 2023 01:42
    0 votes 5 comments
  • ASEReadCounter output for Indels is incorrect
    • Akshay Zawar
    • September 21, 2023 11:36
    0 votes 1 comment
  • Error in running SplitNCigarReads - Attempt to add record to closed writer
    • Valerie Crolley
    • September 18, 2023 16:45
    0 votes 9 comments
  • Error in GATK CollectAllelicCounts
    • Saloni Sinha
    • September 14, 2023 17:27
    0 votes 4 comments
  • PathSeqPipelineSpark multiple cpus
    • Caitlin Newman
    • September 12, 2023 16:39
    0 votes 1 comment
  • Error in MutSigCV on GenePattern
    • HT Liu
    • September 03, 2023 15:06
    0 votes 1 comment
  • Could not find walker with name: DepthOfCoverage
    • Kayleigh Ostberg
    • August 21, 2023 15:11
    • Edited
    0 votes 1 comment
  • Haplotype caller taking too long
    • Rami Kheireddine
    • July 09, 2023 23:43
    0 votes 11 comments
  • problem with R library
    • Laurent MANCHON
    • June 21, 2023 09:38
    0 votes 4 comments
  • PathSeqPipelineSpark successfully but no result
    • Yaer
    • June 09, 2023 06:28
    0 votes 9 comments
  • --minimum-allele-fraction does not work, vcf output is not filtered properly
    • Hiral Desai
    • June 09, 2023 00:11
    0 votes 5 comments
  • Error loading filtermutectcalls.var.vcf.gz in IGV 2.16.0 - htsjdk.samtools.util.RuntimeIOException [file] has invalid uncompressedLength
    • Matteo Costacurta
    • April 12, 2023 23:16
    0 votes 1 comment
  • GaTK-3.3-0 download
    • Walter Tulle
    • March 30, 2023 14:31
    0 votes 2 comments
  • Error in Running command GtcToVcf
    • Nur Adlina Binti Mohd Affian
    • March 29, 2023 05:28
    0 votes 4 comments
  • Question about the allele depth generated by haplotypecaller and ASEReadCounter
    • 杨烁
    • March 27, 2023 09:00
    0 votes 1 comment
  • FastaAlternateReferenceMaker generates same sequence for multisample vcf
    • Kathrin B
    • March 17, 2023 14:09
    0 votes 1 comment
  • GATK ContaminationModel
    • Itai Beno
    • March 15, 2023 16:36
    0 votes 0 comments
  • Error while running HaplotypeCaller
    • Achint Kumar
    • February 19, 2023 13:54
    0 votes 1 comment
  • Picard LiftOver behaviour for multiallelic positions
    • Adeline Morez
    • February 03, 2023 11:22
    0 votes 1 comment
  • ASEReadCounter does not return the value only for chrX
    • Kei Enomoto
    • February 04, 2023 05:07
    • Edited
    0 votes 2 comments
  • ApplyVQSR: "[W::bgzf_read_block] EOF marker is absent" and "[tabix] the index file exists." errors
    • Bob Ye
    • January 25, 2023 23:12
    0 votes 0 comments
  • gatk4-GenotypeGVCFs.nf doens't recognize Primary_000001F chromosomes for process GatherVcfs
    • Carole Couture
    • December 08, 2022 15:19
    0 votes 0 comments
  • HaplotypeCaller confuses introns as long deletions
    • Vladimir Souza
    • November 09, 2022 23:03
    • Edited
    0 votes 4 comments
  • error when running ASEReadCounter
    • behzad
    • October 27, 2022 11:20
    0 votes 2 comments
  • SortSam - Question about I/O error
    • Henry
    • October 27, 2022 08:20
    0 votes 2 comments
  • Does GATK4 BaseRecalibrator not understand relative paths?
    • Eva (Evander)
    • October 17, 2022 12:51
    0 votes 10 comments
  • CombineGVCFs - possible to restart/continue run?
    • medgen
    • October 11, 2022 14:01
    0 votes 5 comments
  • CGA3_WES_Characterization_Pipeline_v0.2_Jun2019 PoN Errors...
    • Rose Gold
    • September 28, 2022 14:32
    0 votes 1 comment
  • GenomeSTRiP SVPreprocess error
    • Jibin Jeong
    • September 15, 2022 04:51
    • Edited
    1 vote 1 comment
  • Genomestrip: Argument with name '--ploidyMapFile' (-ploidyMapFile) is missing
    • Senwei
    • April 27, 2022 07:59
    1 vote 2 comments
  • 1
  • 2
  • 3
  • 4
  • 5
  • 6
  • ›
  • »

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