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Variant Discovery in High-Throughput Sequencing Data

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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

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Somatic

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Show all All Planned Not planned Completed Answered No status Sort by newest post Newest post Recent activity Votes Comments
  • Mutect w/ panel of normal throwing errors, even though mutect w/o panel of normal works fine.
    • Eduardo Maury
    • September 09, 2023 18:45
    0 votes 1 comment
  • Details about the filters used in a previous version of FilterMutectCalls
    • Tal Gutman
    • September 04, 2023 08:13
    0 votes 7 comments
  • Mutect2 overlapping reads behavior with --pcr-snv-qual parameter
    • Semen Leyn
    • September 03, 2023 05:15
    0 votes 2 comments
  • Mutect2 in multisample mode slows at HLA Loci in hg38 alt-aware alignments
    • Nathaniel Alzofon
    • August 29, 2023 04:44
    • Edited
    0 votes 1 comment
  • Mutect2 output False Negative SNV result
    • Danyue Wang
    • August 25, 2023 03:07
    0 votes 6 comments
  • Mutect2 -could not detect expected Indels
    • Shivangi Agarwal
    • August 21, 2023 17:45
    0 votes 2 comments
  • SOLVED: Get read counts of Mutect2 somatic variants
    • Mariana E. M.
    • August 11, 2023 15:17
    • Edited
    1 vote 1 comment
  • Mutect2 -- How is the --max-population-af filter used in tumor-only mode?
    • Layne Rogers
    • July 27, 2023 13:02
    • Edited
    0 votes 1 comment
  • GATK Mutect2 "--germline-resource" and "--panel-of-normals" for reference hg19
    • Manuel Sérgio Sokolov Ravasqueira
    • July 26, 2023 11:39
    • Edited
    0 votes 3 comments
  • Why are some variants not phased in Mutect2
    • xin cui
    • July 25, 2023 07:02
    • Edited
    0 votes 1 comment
  • CalculateContamination error
    • yb87625
    • July 10, 2023 06:08
    • Edited
    0 votes 1 comment
  • how to generate the common site file for hg38 (CNV analysis)
    • yang S
    • July 10, 2023 04:27
    • Edited
    0 votes 2 comments
  • False positive INDELs by Mutect2
    • Safina
    • June 30, 2023 19:53
    • Edited
    0 votes 1 comment
  • Mutect2 - No .stats file created with SLURM
    • Ryan Yordanoff
    • June 20, 2023 23:11
    1 vote 2 comments
  • Mutect2 with HiFi
    • Daphna
    • June 20, 2023 08:34
    0 votes 2 comments
  • normal sample AF in Mutect2 paired mode
    • Fran
    • May 26, 2023 13:13
    0 votes 1 comment
  • MUTECT2 bamout reports far more reads than original bam - reliable?
    • Jana Marie Schwarz
    • May 24, 2023 11:41
    0 votes 1 comment
  • Somatic copy number variants (CNVs) and Panel of Normals creation
    • Indrani Datta
    • May 17, 2023 15:34
    0 votes 6 comments
  • interval list for CNV analysis of samples being sequence using target panel platform
    • yang S
    • April 12, 2023 18:19
    0 votes 3 comments
  • FilterMutectCalls complains about the --ob-prior file's result
    • Thomas Sunghoon Huh
    • April 11, 2023 05:01
    0 votes 4 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
  • GATK 4.3.0.0 Mutect2 fail to call variant Answered
    • yangjw
    • February 17, 2023 00:40
    • Edited
    0 votes 2 comments
  • How to recover a mutation from secondary alignment
    • Laurent MANCHON
    • February 01, 2023 08:41
    0 votes 8 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
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