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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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Show answered All Planned Not planned Completed Answered No status Sort by newest post Newest post Recent activity Votes Comments
  • How does Mutect2 count read depth/coverage? Answered
    • Sameer Shankar
    • February 16, 2023 20:40
    1 vote 11 comments
  • CallCopyRatioSegments -- how does it work? Answered
    • Austin Southard-Smith
    • February 10, 2023 20:46
    0 votes 3 comments
  • Picard SortSam error Answered
    • Tanay Biswas
    • October 14, 2022 11:18
    0 votes 3 comments
  • Issues with LiftoverVcf Answered
    • Mohammad Deen Hayatu
    • October 06, 2022 06:43
    0 votes 6 comments
  • Too many duplicate articles Answered
    • Дмитрий Голик
    • September 09, 2022 09:14
    0 votes 2 comments
  • ASEReadCount Only Outputting the First Chromosome Answered
    • Leslie Youtsey
    • August 31, 2022 19:31
    0 votes 3 comments
  • ASEReadCounter outputting blank table Answered
    • Leslie Youtsey
    • August 24, 2022 17:53
    • Edited
    0 votes 4 comments
  • SamToFastq - bam order Answered
    • Jakub Savara
    • July 24, 2022 10:48
    0 votes 6 comments
  • Limit core use of DetermineGermlineContigPloidy & GermlineCNVCaller Answered
    • Blaz Vrhovsek
    • June 30, 2022 11:27
    1 vote 1 comment
  • HaplotypeCaller using one sample split in two bam files Answered
    • elena vigorito
    • June 28, 2022 09:16
    0 votes 3 comments
  • GATK genomicsDBImport error Answered
    • @OK
    • June 14, 2022 11:11
    0 votes 3 comments
  • germline mutation calling using per-sample module Answered
    • chenglei
    • June 08, 2022 16:06
    0 votes 2 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 3 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
  • Values for QD annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations. Answered
    • tahi
    • February 22, 2022 08:48
    0 votes 1 comment
  • 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 4 comments
  • WDL pipeline: Mitochondrial-short-variant-discovery Answered
    • manolis
    • January 25, 2022 07:57
    0 votes 2 comments
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