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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 votes Newest post Recent activity Votes Comments
  • strand bias and orientation bias
    • that girl
    • December 02, 2020 06:51
    4 votes 1 comment
  • Broad hg38 ICE interval list Answered
    • Chet Birger
    • February 20, 2020 19:16
    3 votes 17 comments
  • Custom made Panel of Normals required?
    • Pedro Miguel Raposo
    • July 07, 2020 10:01
    • Edited
    2 votes 2 comments
  • Generating ACS like output from new GATK CNV pipeline (WGS)
    • Jett Crowdis
    • June 26, 2020 18:11
    2 votes 4 comments
  • Problems in subsampling reads for Mutect2 with --max-reads-per-alignment-start Answered
    • yqiu
    • January 06, 2022 00:13
    • Edited
    1 vote 13 comments
  • empty pon vcf file Answered
    • Lait
    • November 03, 2021 14:32
    1 vote 1 comment
  • Mutect2 issue with --force-active: not all regions are active Answered
    • Maria Litovchenko
    • September 08, 2021 17:29
    1 vote 25 comments
  • Broad hg19 TWIST interval list Answered
    • Tejas Jammihal
    • January 20, 2021 17:14
    1 vote 4 comments
  • Funcotator Errors : I/O error in the advisory file locking logic (disk I/O error)
    • Min-Hwan Sohn
    • November 26, 2020 03:56
    • Edited
    1 vote 1 comment
  • bwa index doesn't create .alt file in hg38 Answered
    • MatZ
    • November 12, 2020 14:15
    1 vote 8 comments
  • How do I merge f1r2.tar.gz files when parallelizing Mutect2 pipeline?
    • Jenifer
    • October 28, 2020 17:25
    • Edited
    1 vote 1 comment
  • MarkDuplicatesSpark error missing Read Group fields
    • Field -Ye Tian
    • October 09, 2020 16:45
    1 vote 1 comment
  • CalculateContamination "there is no such column: contig"
    • Jensen Richardson
    • July 05, 2020 18:02
    1 vote 8 comments
  • gatk CollectAllelicCounts error
    • peterchung
    • May 26, 2020 03:23
    • Edited
    1 vote 6 comments
  • Mutect2 MISSING Low Frequency key (TP53 and KRAS) mutations
    • Saba
    • April 29, 2020 15:54
    • Edited
    1 vote 15 comments
  • Mutect2 - somatic variant calling with/without matched normal sample
    • D B
    • February 26, 2020 19:33
    • Edited
    1 vote 14 comments
  • MergeBamAlignment Error: ArrayIndexOutOfBoundsException
    • Jared Jurss
    • February 19, 2020 22:02
    1 vote 3 comments
  • Problems combining gVCFs that have thousands of scaffolds
    • Dch
    • February 11, 2020 23:24
    • Edited
    1 vote 5 comments
  • Call germline mutations from Mutect2
    • Chadi Saad
    • January 14, 2020 10:30
    1 vote 3 comments
  • ModelSegments not reading allelic counts file Answered
    • Ross Jackson
    • May 11, 2022 06:36
    0 votes 1 comment
  • Error "Could not create tar.gz file" for Mutect2 --f1r2-tar-gz
    • Saya Rene Dennis
    • April 27, 2022 22:37
    0 votes 3 comments
  • ModelSegments - java.lang.IllegalArgumentException: Metadata of the allelic counts and the segments do not match Answered
    • Tony Tan
    • April 19, 2022 02:48
    • Edited
    0 votes 3 comments
  • Error in building panel of normal in somatic copy number variation calling Answered
    • Lei Yu
    • April 04, 2022 21:55
    0 votes 4 comments
  • Contig chr1_KQ031383v1_fix not present in the sequence dictionary Answered
    • zzh
    • March 29, 2022 03:39
    0 votes 5 comments
  • How to create Panel of Normals?
    • Tanay Biswas
    • March 25, 2022 13:16
    • Edited
    0 votes 7 comments
  • FilterMutectCalls 'haplotype' filter value assigned to variants with different PGT tag Answered
    • Francesco Mazzarotto
    • March 23, 2022 14:16
    0 votes 9 comments
  • A USER ERROR has occurred: Duplicate sample: PD4086bv2. Sample was found in both file Answered
    • jesus ix ballote
    • March 04, 2022 20:34
    0 votes 7 comments
  • In Mutect2 force-calling allele via --alleles does not force-call the allele Answered
    • Rahul Gupta
    • February 04, 2022 17:13
    • Edited
    0 votes 14 comments
  • FilterMutectCalls, --distance-on-haplotype and variants filtered for haplotype Answered
    • ElenaGrassi
    • February 03, 2022 10:28
    0 votes 9 comments
  • Read-orientation filter removes tens of thousands of somatic variants after FilterMutectCalls Answered
    • Santiago Sanchez
    • January 25, 2022 18:21
    0 votes 6 comments
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