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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
  • 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
  • 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
  • Variables harmonization tutorial for variables collected from Pic-sure from various cohort
    • kei_hang_chan
    • January 26, 2023 06:18
    0 votes 0 comments
  • Picard's CollectRnaSeqMetrics
    • Benli Chai
    • January 17, 2023 20:36
    0 votes 0 comments
  • Detailed reason for filtering by FilterMutectCalls
    • tan qiang
    • January 13, 2023 07:44
    0 votes 0 comments
  • How to specify number of threads while running Mutect2
    • Tanay Biswas
    • December 21, 2022 05:49
    0 votes 0 comments
  • Best practice trios
    • Sheryl
    • November 23, 2022 00:58
    • Edited
    0 votes 0 comments
  • BuildBamIndex
    • Robert Bremel
    • November 08, 2022 20:27
    0 votes 4 comments
  • Java exception: index 65 is CONSTANT_MethodRef and should be CONSTANT_InterfaceMethodRef
    • Julián García-Abadillo
    • October 27, 2022 13:37
    • Edited
    0 votes 2 comments
  • Can't access google cloud it says permission required
    • HQ Zhao
    • October 27, 2022 02:03
    0 votes 2 comments
  • RGID versus RGPU
    • Jean-Michel Carter
    • October 20, 2022 06:49
    • Edited
    0 votes 1 comment
  • Picard SortSam error Answered
    • Tanay Biswas
    • October 14, 2022 11:18
    0 votes 3 comments
  • Mutect2 produces 0 results for somatic mutation calling of paired-end reads (BAM)
    • Di Pan
    • October 09, 2022 05:22
    • Edited
    0 votes 1 comment
  • Issues with LiftoverVcf Answered
    • Mohammad Deen Hayatu
    • October 06, 2022 06:43
    0 votes 6 comments
  • Documentation for interval files in resource bundle
    • Laura Egolf
    • September 19, 2022 21:28
    0 votes 1 comment
  • UmiAwareMarkDuplicatesWithMateCigar - UMI_METRICS
    • Miguel Grau
    • September 13, 2022 10:55
    • Edited
    0 votes 2 comments
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