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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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  • Funcotator errors
    • MPetlj
    • August 05, 2020 23:40
    0 votes 27 comments
  • Incorrect alleles reported by Mutect2
    • Guruprasad Ananda
    • August 05, 2020 17:44
    • Edited
    0 votes 1 comment
  • Issue with output from CollectAllelicCounts
    • jejacobs23
    • August 04, 2020 22:01
    0 votes 1 comment
  • How can i remove chr_Un* from somatic cnv plots?
    • sahuno
    • July 29, 2020 12:56
    • Edited
    0 votes 2 comments
  • Mutect2, force-calling-mode, and restricting calls to positions in force-call-alleles.vcf
    • Robert Dubin
    • July 28, 2020 20:27
    0 votes 3 comments
  • GenomicsDBImport genomicsdb-workspace-path not recognized
    • Lance Heady
    • July 27, 2020 18:28
    0 votes 3 comments
  • Mutect2 output - resources?
    • MPetlj
    • July 27, 2020 15:47
    0 votes 4 comments
  • error: read goes past end of reference
    • Wout Megchelenbrink
    • July 24, 2020 14:08
    0 votes 5 comments
  • munmap_chunk(): invalid pointer [FilterAlignmentArtifacts task in mutetct2 workflow]
    • sahuno
    • July 24, 2020 10:03
    0 votes 5 comments
  • Mutect2's support for MNP in GATK 4.1.8.1?
    • Bing
    • July 23, 2020 01:29
    0 votes 3 comments
  • CrosscheckFingerprints EXIT_CODE_WHEN_MISMATCH doesn't seem to work
    • Alijah O'Connor
    • July 22, 2020 17:32
    0 votes 2 comments
  • Mutect2 multi-sample pipeline
    • manolis
    • July 20, 2020 14:04
    0 votes 13 comments
  • Mutect2 PoN best practice pipeline failed with GenomicsDBImport 'A USER ERROR has occurred: Failed to create reader from file' ERROR
    • WangZiwei
    • August 07, 2020 07:21
    • Edited
    0 votes 10 comments
  • GATK pipeline from which repository (gatk-workflows or broadinstitute/gatk) should I use?
    • WangZiwei
    • July 20, 2020 07:28
    0 votes 5 comments
  • Mutect2 PoN best practice pipeline failed with GenomicsDBImport 'A USER ERROR has occurred: Failed to create reader from file' ERROR
    • WangZiwei
    • July 20, 2020 04:55
    • Edited
    0 votes 3 comments
  • Mutect2 for ultrasensitive low coverage calling
    • Arvind Ravi
    • July 17, 2020 13:47
    0 votes 2 comments
  • SAMException: Value was put into PairInfoMap error even after using -M flag
    • rohit satyam
    • July 15, 2020 07:01
    • Edited
    0 votes 5 comments
  • High number of transversions after running Mutect2 and FilterMutectCalls on WES data
    • Paul-Arthur Meslin
    • July 09, 2020 16:33
    • Edited
    0 votes 3 comments
  • I can't make FastaAlternateReferenceMaker works
    • Luca Stefanucci
    • July 09, 2020 14:00
    0 votes 4 comments
  • Error using output of ScatterIntervalsByNs by SplitIntervals
    • Kristian Unger
    • July 07, 2020 20:45
    0 votes 1 comment
  • CalculateContamination "there is no such column: contig"
    • Jensen Richardson
    • July 05, 2020 18:02
    1 vote 8 comments
  • Custom made Panel of Normals required?
    • Pedro Miguel Raposo
    • July 07, 2020 10:01
    • Edited
    2 votes 2 comments
  • A JAVA Error when running GATKSVPipelineBatch.wdl with GATKSVPipelineBatch.ref_panel_1kg.json
    • 2tong
    • July 01, 2020 04:39
    0 votes 1 comment
  • Mutect2 false negatives
    • myourshaw
    • June 29, 2020 19:31
    • Edited
    0 votes 1 comment
  • Generating ACS like output from new GATK CNV pipeline (WGS)
    • Jett Crowdis
    • June 26, 2020 18:11
    2 votes 4 comments
  • Mutect2 --alleles param GATK_4.1.7.0
    • registered_user
    • June 26, 2020 14:54
    • Edited
    0 votes 2 comments
  • filtervariant in GATK 3.8
    • Bipin Chand
    • June 26, 2020 07:20
    0 votes 1 comment
  • Mutect2 parallelize input
    • alanhoyle
    • June 25, 2020 14:45
    0 votes 4 comments
  • Why no overlaps between shifted variants and non-shifted variants in gatk4-mitochondria-pipeline? (Mutect2)
    • Changhan Yoon
    • June 24, 2020 08:06
    • Edited
    0 votes 1 comment
  • Mutect2-PON Storage object issue when running across multiple samples?
    • MPetlj
    • June 22, 2020 15:57
    0 votes 30 comments
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