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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
  • GenotypeGVCFs runtime extremely long and not starting at 0%
    • Cindy Li
    • June 15, 2020 17:34
    0 votes 1 comment
  • Mutect tumor-only vs matched normal calls? Answered
    • vctrymao
    • June 09, 2020 23:07
    0 votes 2 comments
  • (MultiSample Mode) Somatic Variants PASSed with zero Normal Coverage
    • Zachary Weber
    • June 09, 2020 17:53
    • Edited
    0 votes 2 comments
  • Mutect2 Funcotator error
    • MPetlj
    • June 08, 2020 16:15
    0 votes 31 comments
  • Assignment of Read group for Ion Torrent reads
    • 加藤啓輔
    • June 08, 2020 15:51
    0 votes 1 comment
  • AnalyzeCovariates Answered
    • Lucas Kopecky Bobadilla
    • June 05, 2020 15:53
    0 votes 9 comments
  • Mutect2 PON - gnomAD input?
    • MPetlj
    • June 03, 2020 14:36
    0 votes 18 comments
  • Funcotator Appears to have completed but with RunTimeException
    • Robert Bremel
    • June 03, 2020 13:20
    0 votes 4 comments
  • Option "--dont-use-soft-clipped-bases" does not seem to work in Mutect2
    • janrehker
    • June 02, 2020 13:25
    • Edited
    0 votes 13 comments
  • When calling with polyN region of right mapping lead to loss of true pathogenic snp site
    • Xin Zheng
    • June 02, 2020 06:27
    • Edited
    0 votes 1 comment
  • Running GATK funcotator on cluster
    • Amit
    • May 28, 2020 20:13
    0 votes 10 comments
  • sgz used in tumor-only model
    • that girl
    • May 27, 2020 06:09
    0 votes 10 comments
  • Error during generation of Generate a CNV panel of normals with CreateReadCountPanelOfNormals
    • Joan Chen
    • May 26, 2020 19:34
    0 votes 2 comments
  • gatk CollectAllelicCounts error
    • peterchung
    • May 26, 2020 03:23
    • Edited
    1 vote 6 comments
  • Mutect2 missing variant
    • Enrico Cocchi
    • May 23, 2020 23:06
    0 votes 3 comments
  • Functotator - I/O error in the advisory file locking logic
    • anirudh modi
    • May 23, 2020 13:06
    0 votes 1 comment
  • GenomeSTRiP CNVDiscovery error
    • Thandeka
    • May 22, 2020 18:43
    0 votes 7 comments
  • Using VSQR for somatic mutations?
    • vctrymao
    • May 21, 2020 17:59
    0 votes 8 comments
  • true somatic mutation not called by mutect2
    • mingming liu
    • May 21, 2020 10:01
    0 votes 1 comment
  • GATK HaplotypeCaller (v 4.1.7.0)--alleles
    • nonesense
    • May 19, 2020 23:36
    0 votes 3 comments
  • How should I deal with tandem repeat?
    • Su Na
    • May 19, 2020 03:41
    0 votes 2 comments
  • mutect2 realignment
    • Qing Zhang
    • May 18, 2020 17:50
    0 votes 3 comments
  • Increased number of false positives in Mutect2 GATK 4.1.7.0
    • registered_user
    • May 18, 2020 12:53
    • Edited
    0 votes 13 comments
  • Command Gatk not found
    • Tania Zahid
    • May 17, 2020 09:10
    • Edited
    0 votes 4 comments
  • Whole genome Pooled sequnce data analysis
    • Tania Zahid
    • May 17, 2020 09:04
    • Edited
    0 votes 1 comment
  • Somatic - Not cancer - RNA
    • Peter Kilfeather
    • May 15, 2020 17:18
    0 votes 5 comments
  • Fake panel of normal performs better than publicly available in variant calling tumor-only samples
    • mariesmith
    • May 14, 2020 12:47
    0 votes 5 comments
  • PoN: Mutect2 error
    • manolis
    • May 13, 2020 04:34
    0 votes 7 comments
  • SplitIntervals Random or Not?
    • vctrymao
    • May 12, 2020 17:31
    0 votes 2 comments
  • Using LearnReadOrientationModel produces new mutations?
    • vctrymao
    • May 11, 2020 22:55
    0 votes 2 comments
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