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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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Documentation Questions

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Show all All Planned Not planned Completed Answered No status Sort by votes Newest post Recent activity Votes Comments
  • Known Sites for BQSR Answered
    • T. Li
    • December 07, 2020 22:26
    5 votes 5 comments
  • How does Mutect2 count read depth/coverage? Answered
    • Sameer Shankar
    • February 16, 2023 20:40
    2 votes 11 comments
  • Difference between the different annotation groups available in GATK
    • Shashank Nagaraja
    • October 04, 2021 22:15
    2 votes 1 comment
  • Where is the list of annotations and annotation groups? Answered
    • tedtoal
    • July 05, 2021 23:05
    2 votes 7 comments
  • gCNV
    • Sabrina Camp
    • June 24, 2020 10:13
    2 votes 1 comment
  • GATK4.1.5 GenotypeGVCFs --annotation-group
    • hana lango allen
    • March 12, 2020 16:06
    2 votes 1 comment
  • HOW TO EXCLUDE FILTERED VARIANTS WITH VARIANTFILTRATION?
    • Rômulo Carleial
    • July 07, 2023 12:46
    1 vote 1 comment
  • License / use terms for GATK resource bundle
    • Mariana E. M.
    • July 04, 2023 10:17
    1 vote 2 comments
  • Explanation on the HS Penalty metric
    • Pierre_Bioinfo
    • April 20, 2023 07:51
    1 vote 3 comments
  • Genotype filtering still write "PASS" in filter field
    • Marissa Eronika
    • March 21, 2023 15:50
    1 vote 7 comments
  • Report file CreateExtendedIlluminaManifest Report file
    • James Gallant
    • October 31, 2022 15:28
    1 vote 1 comment
  • Limit core use of DetermineGermlineContigPloidy & GermlineCNVCaller Answered
    • Blaz Vrhovsek
    • June 30, 2022 11:27
    1 vote 1 comment
  • Documentation for running GATK and Cromwell on IBM Cloud Answered
    • Takeshi Yoshimura
    • April 05, 2022 01:24
    1 vote 7 comments
  • genotyping calls don't align with coverage Answered
    • Gertjan Wils
    • March 15, 2022 12:57
    1 vote 1 comment
  • Confirmation that Mutect2 /haplotype caller only use reads mapped within the active region
    • JW
    • June 03, 2021 16:19
    1 vote 3 comments
  • Where do I find guidance on when to mark duplicates a second time? Answered
    • ISmolicz
    • November 13, 2020 11:54
    1 vote 2 comments
  • Germline Resouce Answered
    • happyhihello
    • July 31, 2020 17:23
    1 vote 3 comments
  • How to find or generate common germline variant sites VCF required by GetPileupSummaries
    • Antti Koskenalho
    • May 27, 2020 06:22
    1 vote 4 comments
  • CollectAllelicCounts interval_list Answered
    • jejacobs23
    • May 18, 2020 22:33
    1 vote 15 comments
  • vcf files for BQSR step Answered
    • Varun Gupta
    • March 30, 2020 22:13
    1 vote 4 comments
  • GATK Best Practices Mitochondrial Analysis Answered
    • ajwils
    • January 09, 2020 21:15
    • Edited
    1 vote 45 comments
  • Select Variants
    • Patrick Bianchi
    • November 29, 2023 10:29
    0 votes 2 comments
  • GATK problem with the CombineGVCFs
    • David Sanchez Sotomayor
    • November 20, 2023 21:26
    0 votes 1 comment
  • How to use the --alleles option of HaplotypeCaller ?
    • Chloé Girard
    • November 10, 2023 16:58
    • Edited
    0 votes 8 comments
  • Picard MarkDuplicates Functionality
    • Nagashree Rachote
    • October 23, 2023 12:51
    0 votes 1 comment
  • Missing documentation on somatic variant calling output VCF
    • Fia
    • October 22, 2023 20:55
    0 votes 1 comment
  • MergeMutectStats missing from documentation
    • G E
    • October 20, 2023 02:01
    0 votes 1 comment
  • What is the recommended way to use/parse Funcotator output?
    • Steffen Møller Bøttger
    • October 11, 2023 10:52
    • Edited
    0 votes 1 comment
  • Maximum number of Plasma samples by use mutect2 multi-sample pipeline
    • Jiao Zhang
    • September 20, 2023 01:50
    • Edited
    0 votes 2 comments
  • GATK Funcotator MAF header
    • Gregory Joseph
    • September 19, 2023 21:13
    0 votes 1 comment
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