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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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  • GGA-mode gives PASS tag while the site failed in the normal workflow
    • xiucz
    • November 16, 2021 03:22
    • Edited
    0 votes 13 comments
  • Error while running ModelSegments Answered
    • onurerdoganmd
    • November 09, 2021 20:52
    0 votes 3 comments
  • Mutect2 Funcotator interval error Answered
    • Elise Valkanas (she/her)
    • November 09, 2021 15:39
    • Edited
    0 votes 5 comments
  • Called Somatic Mutations High Frequency of C>A SNVs Answered
    • Jeremy Huang
    • November 04, 2021 14:46
    • Edited
    0 votes 6 comments
  • empty pon vcf file Answered
    • Lait
    • November 03, 2021 14:32
    1 vote 1 comment
  • Funconator's ignore-filtered-variants is not a recognized option Answered
    • Stephen Chung
    • October 26, 2021 15:16
    0 votes 1 comment
  • missing file: Callset.json , when creating PON Answered
    • Lait
    • October 22, 2021 10:13
    0 votes 3 comments
  • MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true does not add DS and DI tags in the output BAM file Answered
    • Adeline Morez
    • October 22, 2021 09:44
    • Edited
    0 votes 3 comments
  • SAMException: Value was put into PairInfoMap more than once Answered
    • Mohammad Tanhaemami
    • October 21, 2021 13:43
    • Edited
    0 votes 5 comments
  • Why do I see a variant called by mutect2 in my matched-normal sample when checking the results? Answered
    • Jenifer
    • October 20, 2021 11:34
    • Edited
    0 votes 10 comments
  • Mutect2 calls long deletion with absolutely zero read support Answered
    • Brian Wiley
    • October 19, 2021 00:53
    0 votes 1 comment
  • Deletion is split into two deletions Answered
    • Maximilian Dörrbecker
    • October 05, 2021 08:07
    0 votes 1 comment
  • Mutect2 bamout reports fewer reference reads than original bam, causing false positive call.
    • CYWang
    • October 03, 2021 11:30
    0 votes 7 comments
  • Why do I get ‘Badly formed genome unclippedLoc: Contig chrY given as location, but this contig isn't present in the Fasta sequence dictionary’ when running GetPileupSummaries?
    • Ruiqiao Bai
    • September 26, 2021 08:20
    0 votes 7 comments
  • Running Mutect 2 with matched normal vs tumor mode
    • Mommy Misato
    • September 17, 2021 17:23
    0 votes 3 comments
  • Why do I get 'java.lang.IllegalArgumentException: Dictionary cannot have size zero' when using GetPileupSummaries? Answered
    • Ruiqiao Bai
    • September 12, 2021 01:06
    0 votes 12 comments
  • Not generating denoisedLimit4.png with PlotModeledSegments
    • Hanyin Wang
    • September 10, 2021 07:23
    0 votes 4 comments
  • Mutect2 issue with --force-active: not all regions are active Answered
    • Maria Litovchenko
    • September 08, 2021 17:29
    1 vote 25 comments
  • Incorrect Annotation from Funcotator Answered
    • Hanbing Song
    • August 26, 2021 00:49
    0 votes 5 comments
  • merge nearby variants in vcf from mutect2 Answered
    • Junfeng Jiang
    • August 12, 2021 14:36
    • Edited
    0 votes 1 comment
  • gatk stack memory insufficient to run Mutect2 for artifact correction Answered
    • Uma Saxena
    • August 09, 2021 13:01
    • Edited
    0 votes 1 comment
  • Mutect2 genotype-germline-sites filtering discrepancy Answered
    • TA
    • July 26, 2021 18:24
    0 votes 4 comments
  • Error running mutect2 on SAM files remapped to hg38 (original reads were aligned to hg19). Answered
    • zdr j
    • July 17, 2021 05:24
    • Edited
    0 votes 1 comment
  • Missing Variants from Panel of Normals Answered
    • Dave Sims
    • July 16, 2021 17:35
    • Edited
    0 votes 2 comments
  • GetPileupSummaries Answered
    • Mommy Misato
    • July 14, 2021 21:17
    0 votes 5 comments
  • Mutect2 PoN - GenomicsDBImport creates empty DB Answered
    • Enrico Cocchi
    • July 14, 2021 10:37
    • Edited
    0 votes 15 comments
  • Created panel of normals returns empty vcf Answered
    • Rafael Viana
    • July 05, 2021 15:04
    0 votes 3 comments
  • selecting allele depth Mutect2 Answered
    • Sonia Wolf
    • June 28, 2021 17:39
    0 votes 1 comment
  • The mutect ERROR:Please add an explicit type tag :NAME listing the correct type from among the supported types Answered
    • 灵己 孟
    • June 28, 2021 03:15
    0 votes 3 comments
  • Error while running CreateReadCountPanelOfNormals with gatk-4.1.4.1 Answered
    • Alice Shen
    • June 10, 2021 07:36
    0 votes 3 comments
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