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. Somatic

Somatic

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
  • Huge number of variants in tumor only mode as compared to T/N paired mode using Mutect2
    • Shivangi Agarwal
    • March 09, 2023 22:26
    0 votes 3 comments
  • Somatic CNV Workflow Tutorials
    • Yuwei Bao
    • March 02, 2023 20:45
    0 votes 1 comment
  • Mutect2 VCF out Tumor Normal
    • Charitra K
    • March 01, 2023 07:53
    0 votes 5 comments
  • Strange differences in detected variants called by mutect2 --dont-use-soft-clipped-bases true vs false
    • Jana Marie Schwarz
    • February 22, 2023 16:26
    0 votes 1 comment
  • How to recover a mutation from secondary alignment
    • Laurent MANCHON
    • February 01, 2023 08:41
    0 votes 2 comments
  • Is it ok to use -L for each chromosome separately when running Mutect2?
    • Xuning Wang
    • January 30, 2023 21:41
    0 votes 1 comment
  • Asking for advice on Mutect2 calling in somatic but amplicon data
    • yangjw
    • January 30, 2023 07:32
    • Edited
    0 votes 2 comments
  • How to call somatic variants without normal matched sample (cfDNA)
    • Abel G
    • January 26, 2023 11:45
    0 votes 0 comments
  • Somatic mutations detection using mutect2
    • Varun Gupta
    • January 23, 2023 16:17
    0 votes 0 comments
  • GatherPileupSummaries does not sort input variants
    • Evan Wu
    • January 20, 2023 23:00
    0 votes 0 comments
  • Problem generating germline resource file for Mutect2
    • Jaime Schwoch
    • January 04, 2023 01:51
    0 votes 0 comments
  • Mutect2 VCF sample order in tumor normal paired call
    • Thomas Sunghoon Huh
    • December 20, 2022 08:49
    0 votes 0 comments
  • How do if remove Germline Variants from my variant calling file ?
    • Seke Keretsu
    • December 08, 2022 21:23
    0 votes 0 comments
  • Error - Mutect2 PG tag
    • A
    • December 08, 2022 02:56
    0 votes 0 comments
  • sample size for somatic CNV
    • Muntadher Jihad
    • December 02, 2022 12:04
    0 votes 1 comment
  • GatherVCFs error - provider not installed
    • kvn95ss
    • December 02, 2022 10:19
    0 votes 1 comment
  • In case there is no vcf file from genome project, is it still possible to use the  GetPileupSummaries?
    • Arye Harel
    • November 15, 2022 15:54
    • Edited
    0 votes 4 comments
  • af-only-gnomad.vcf.gz
    • Shivangi Agarwal
    • November 07, 2022 22:36
    0 votes 1 comment
  • Could not find vcf.stats file after Mutect2
    • Seke Keretsu
    • November 02, 2022 01:15
    0 votes 4 comments
  • Panel of Normals - inconsistent filtering behavior
    • Paula Berry
    • October 18, 2022 16:22
    • Edited
    0 votes 4 comments
  • Create Panel of Normals Issue
    • Yuwei Bao
    • October 12, 2022 00:51
    0 votes 2 comments
  • Can Mutect2 calls tumor sample specific SNV under joint calling mode?
    • Duo Xie
    • August 31, 2022 23:34
    • Edited
    0 votes 3 comments
  • Diferencia entre varinates detectadas usando gatk 4.1.8.1 y 4.1.9.0
    • Nefté Yañez
    • August 29, 2022 07:23
    0 votes 1 comment
  • Issue when running BaseRecalibrator
    • Duo Xie
    • August 20, 2022 16:16
    0 votes 5 comments
  • GATK4 Somatic CNV - proportional coverage calculation blunted
    • Kevin Meli
    • August 17, 2022 20:30
    0 votes 1 comment
  • Issue with MergeBamAlignment
    • Javier
    • July 21, 2022 19:28
    0 votes 0 comments
  • Funcotator maf has different alt allele than vcf for some variants
    • Balthasar
    • July 11, 2022 11:34
    1 vote 1 comment
  • Funcotator Custom Annotation Table Not Working
    • Etienne Mahe
    • July 04, 2022 01:39
    0 votes 4 comments
  • Error "Could not create tar.gz file" for Mutect2 --f1r2-tar-gz
    • Saya Rene Dennis
    • April 27, 2022 22:37
    0 votes 3 comments
  • How to create Panel of Normals?
    • Tanay Biswas
    • March 25, 2022 13:16
    • Edited
    0 votes 7 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