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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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Documentation Questions

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  • GATK genomicsDBImport error Answered
    • @OK
    • June 14, 2022 11:11
    0 votes 3 comments
  • Haplotypecaller Answered
    • Mahdi Ahmadi
    • May 30, 2022 16:45
    0 votes 1 comment
  • BaseRecalibrator --max-cycle Answered
    • oğuzhan karaosmanoğlu
    • May 12, 2022 11:11
    0 votes 1 comment
  • Question on Java version Answered
    • Anand
    • May 10, 2022 15:24
    0 votes 2 comments
  • GATK CNV somatic panels of normal design Answered
    • Mallika Gandham
    • May 04, 2022 16:07
    0 votes 2 comments
  • JointGermlineCNVSegmentation Answered
    • Yangyxt
    • April 30, 2022 06:56
    0 votes 2 comments
  • GetPileupSummaries common germline variant sites VCF hg38 Answered
    • Anish K
    • April 18, 2022 16:48
    0 votes 2 comments
  • Documentation for running GATK and Cromwell on IBM Cloud Answered
    • Takeshi Yoshimura
    • April 05, 2022 01:24
    1 vote 7 comments
  • how to run "gatk-register"? Answered
    • Mahendra Singh
    • March 28, 2022 04:28
    0 votes 2 comments
  • MergeBamAlignment for mitochondrial variant discovery Answered
    • Ahmed S. Chakroun
    • March 18, 2022 17:33
    0 votes 1 comment
  • genotyping calls don't align with coverage Answered
    • Gertjan Wils
    • March 15, 2022 12:57
    1 vote 1 comment
  • Is FilterAlignmentArtifacts out of the Mutect2 calling best practices? Answered
    • shenglai
    • March 11, 2022 01:53
    0 votes 1 comment
  • MergeBamAlignment conflicting headers between mapped and unmapped Answered
    • TA
    • March 04, 2022 15:13
    0 votes 3 comments
  • VariantsToTable not working Answered
    • Arwa Ahmad
    • February 25, 2022 08:56
    0 votes 2 comments
  • GATK GenotypeGVCFs miss a real Insertion Answered
    • touyupang
    • February 18, 2022 07:45
    0 votes 6 comments
  • How to evlauate the result: GenotypeConcordance or Concordance Answered
    • lizhichao
    • February 17, 2022 09:09
    0 votes 6 comments
  • Mitochondrial shifted reference Answered
    • MARC TORMO PUIGGROS
    • January 26, 2022 10:57
    0 votes 2 comments
  • WDL pipeline: Mitochondrial-short-variant-discovery Answered
    • manolis
    • January 25, 2022 07:57
    0 votes 2 comments
  • GenomicsDBImport -L [string] (but for the whole genome): purpose to generate invariant sites Answered
    • Pete Thorpe
    • January 20, 2022 08:51
    0 votes 8 comments
  • stand_call_conf and stand_emit_conf in GATK 4.2.4.1 Answered
    • M.R-E.H
    • January 17, 2022 16:05
    0 votes 1 comment
  • Mosaic gCNVs with GATK Answered
    • Naga
    • January 13, 2022 17:32
    • Edited
    0 votes 1 comment
  • Why don't I have access to some links? Answered
    • Manuel
    • January 12, 2022 11:13
    0 votes 1 comment
  • "main" java.lang.OutOfMemoryError: Requested array size exceeds VM limit Answered
    • 蒲鹏
    • January 12, 2022 10:12
    0 votes 4 comments
  • CollectReadCounts tutorial incorrectly states default read quality threshold Answered
    • simon lee
    • December 14, 2021 04:06
    • Edited
    0 votes 1 comment
  • "NotDuplicateReadFilter" behaviour in HaplotypeCaller Answered
    • sanjeevksh
    • December 07, 2021 21:40
    0 votes 3 comments
  • Append GenomicsDBimport Answered
    • wbsimey
    • November 18, 2021 18:26
    • Edited
    0 votes 3 comments
  • picard sortvcf: what does it do? Answered
    • Thomas Juettemann
    • November 09, 2021 17:31
    0 votes 7 comments
  • VariantsToTable GT not extracting correctly Answered
    • Asha Mehta
    • October 15, 2021 19:59
    • Edited
    0 votes 1 comment
  • FilterFuncotations Duplicate key error Answered
    • Azza Ahmed
    • October 14, 2021 10:53
    0 votes 7 comments
  • haplotypeCaller phasing Answered
    • Jeremie Kalfon
    • October 05, 2021 15:07
    • Edited
    0 votes 11 comments
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