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. General Discussion

General Discussion

Follow New posts New posts and comments

Show all All Planned Not planned Completed Answered No status Sort by newest post Newest post Recent activity Votes Comments
  • Hi, i am beginner in bioinformatics and need help in how i can index the <fa ref gene file> to accept it , i tried samtools faidx to make .fai file but It didn't do anything about the problem.
    • Mina Ashraf
    • March 26, 2023 08:58
    0 votes 1 comment
  • GATK pathseq reference database availability
    • Ruiwen Zhou
    • March 20, 2023 15:44
    0 votes 1 comment
  • Can DRAGEN-GATK be applied to DNBSEQ?
    • rq m
    • March 19, 2023 03:02
    0 votes 1 comment
  • variant calling on scRNAseq
    • ahlem frigui
    • March 17, 2023 10:49
    0 votes 1 comment
  • ukb - Merging Y chromosome VCF file having different number of samples
    • Shashank Shekhar Padhi
    • March 10, 2023 08:03
    0 votes 2 comments
  • Question about handling genotypes during VCF liftOver from hg38 to hg19 using LiftoverVCF command
    • user105689
    • March 07, 2023 20:54
    0 votes 1 comment
  • Question on using GATK-DRAGEN (dragmap-os aligner) with Mutect2
    • Anand
    • March 07, 2023 02:20
    • Edited
    0 votes 1 comment
  • Minimum median mapping quality output query
    • smk_84
    • March 03, 2023 19:42
    0 votes 3 comments
  • Empty, meaningless HaploytypeCaller output
    • Daniel Richard
    • March 02, 2023 22:49
    0 votes 1 comment
  • MarkDuplicatesSpark only supports singleton fragments and pairs. We found the following group with >2 primary reads
    • rohit satyam
    • March 02, 2023 11:45
    • Edited
    0 votes 1 comment
  • Need help with converting VCF to SEG file for CNV visualization Answered
    • Sophia
    • March 01, 2023 15:32
    0 votes 3 comments
  • GATK pathseq - viladation BLASTN
    • Anna Antonatou
    • February 22, 2023 13:51
    0 votes 2 comments
  • VQSR first step do not generate plots
    • Yousef_genetics
    • February 17, 2023 21:12
    0 votes 1 comment
  • Gene coverage issue in GATK 4.3.0.0 using GRCh38
    • Rajesh Kumar Maurya
    • February 20, 2023 04:27
    • Edited
    0 votes 2 comments
  • java.lang.NullPointerException with GenotypeGVCFs on pooled samples
    • Anna Dahlgren
    • February 10, 2023 15:53
    0 votes 1 comment
  • Gene annonation from aligned genome with reference
    • Nagarajan Raju
    • January 30, 2023 18:26
    0 votes 0 comments
  • Extract reads from BAM file that contain specific variant
    • DC
    • January 29, 2023 19:54
    0 votes 0 comments
  • Error in LiftOverIntervalList
    • Ben Oppenheimer
    • January 26, 2023 19:18
    0 votes 0 comments
  • base recalibration
    • Laurent MANCHON
    • January 26, 2023 14:08
    0 votes 0 comments
  • Question about how to run CrossCheckFingerPrints (Haplotype map)
    • Uri David Akavia
    • January 25, 2023 10:33
    0 votes 1 comment
  • --max-events-in-region in FilterMutectCalls
    • Varun Gupta
    • January 24, 2023 17:15
    0 votes 0 comments
  • Pipeline for calling human haloplex fastq's with GATK
    • Amy Houseman
    • January 24, 2023 14:45
    0 votes 0 comments
  • What is RMSMappingQuality formula
    • zhang
    • January 14, 2023 09:58
    • Edited
    0 votes 0 comments
  • No output table for BaseRecalibrator
    • Abigail Sequeira
    • January 13, 2023 20:05
    0 votes 0 comments
  • What are the plans for Funcotator?
    • Pieter Lukasse
    • January 11, 2023 13:41
    0 votes 2 comments
  • Exception in thread "main" java.lang.IllegalArgumentException: Do not use this function to merge dictionaries with different sequences in them. Sequences must be in the same order as well
    • richard.wei
    • January 11, 2023 08:26
    0 votes 9 comments
  • How do I speed up SelectVariants and CountVariants?
    • Joe
    • January 10, 2023 15:28
    0 votes 3 comments
  • GenomicsDBImport-Syntax error in JSON file
    • Tanay Biswas
    • January 06, 2023 08:15
    0 votes 5 comments
  • Using 1 available threads, but 32 were requested [Mutect2]
    • Juan José Garcés Latre
    • December 30, 2022 09:30
    0 votes 0 comments
  • Is it necessory to mention disable-read-filter in Mutect2 somatic calling?
    • Tanay Biswas
    • December 21, 2022 06:00
    0 votes 0 comments
  • 1
  • 2
  • 3
  • 4
  • 5
  • 6
  • ›
  • »

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