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Genome Analysis Toolkit

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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Show all All Planned Not planned Completed Answered No status Sort by newest post Newest post Recent activity Votes 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
  • MuTect2 Mismatch between the reference haplotype and the reference assembly graph path. Answered
    • Heejun Jang
    • June 07, 2021 02:53
    0 votes 1 comment
  • The output of Mutect2 cannot be accepted by FilterMutectCalls in GATK-4.2.0.0 Answered
    • Qihan Long
    • June 04, 2021 03:25
    • Edited
    0 votes 10 comments
  • The depth of SNV/InDels calculated by Mutect2 in GATK4.2.0.0 is much lower than real sequencing depth, why? Answered
    • Ce Wang
    • May 25, 2021 06:08
    • Edited
    0 votes 18 comments
  • How do I set less stringent germline filtering in Mutect2 / filtermutectcalls, many false negatives Answered
    • Tjitske de Vries
    • May 21, 2021 09:47
    0 votes 1 comment
  • Mysterious Funcotator issue Answered
    • Robert Bremel
    • May 21, 2021 01:22
    0 votes 7 comments
  • MergeBamAlignment produces unknown error Answered
    • vctrymao
    • May 18, 2021 16:19
    • Edited
    0 votes 4 comments
  • CollectAllelicCounts- Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded Answered
    • rahelp
    • May 16, 2021 13:17
    0 votes 12 comments
  • IlluminaBasecallsToSam does not demultiplex NovaSeq barcoded reads Answered
    • myourshaw
    • May 10, 2021 21:46
    • Edited
    0 votes 5 comments
  • java.lang.OutofMemoryError: GC overhead limit exceeded Answered
    • Jack Prazich
    • May 03, 2021 16:54
    0 votes 28 comments
  • GenomicsDBImport does not support GVCFs with MNPs Answered
    • Rodolfo Adrián Arriaga Rivera
    • April 23, 2021 16:52
    • Edited
    0 votes 1 comment
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