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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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Show all All Planned Not planned Completed Answered No status Sort by newest post Newest post Recent activity Votes Comments
  • When the useful PGT and PID fields have been implemented in GATK tool for the first time
    • Sandrine lagarrigue
    • December 31, 2020 17:36
    0 votes 1 comment
  • How to merge approx 150 bam file using Picard
    • Abrish
    • December 27, 2020 14:02
    0 votes 4 comments
  • DepthOfCoverage in GATK4.1.9.0 with -gene-list option
    • David Jaspez
    • December 21, 2020 17:36
    • Edited
    0 votes 4 comments
  • Clarity on Variant Callers being "optimized for UMI-containing data"
    • Alijah O'Connor
    • December 18, 2020 00:49
    • Edited
    0 votes 1 comment
  • Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded when using gatk GetPileupSummaries
    • Will
    • December 17, 2020 16:02
    0 votes 1 comment
  • BQSR no output table found
    • Tamrin Chowdhury
    • December 17, 2020 07:20
    0 votes 3 comments
  • How do I get intermediate outputs from cromwell
    • Matthias De Smet
    • December 15, 2020 09:59
    0 votes 1 comment
  • Missing ReadPosRankSum, MQRankSum and BaseQRankSum Scores in VCF
    • Hamza Umut Karakurt
    • December 14, 2020 08:33
    0 votes 1 comment
  • Call-caching not functional running cromwell locally on GCP VM Answered
    • ibrahimkurt
    • December 08, 2020 16:40
    0 votes 9 comments
  • HaplotypeCaller - Shutting down engine - Encountering a large genome
    • zyw
    • December 07, 2020 02:27
    0 votes 5 comments
  • Errors with CNNScoreVariants and HaplotypeCaller: java.nio.BufferUnderflowException
    • WKaiser
    • December 03, 2020 16:11
    0 votes 3 comments
  • GenomicsDBImport: can different VCF files be imported into one genomicsdb workspace against different interval lists?
    • ISmolicz
    • December 02, 2020 17:43
    0 votes 2 comments
  • Some stop positions of .interval_list is smaller than the start positions
    • Shiva Kazempour
    • December 02, 2020 15:35
    0 votes 2 comments
  • GermlineCNVCaller edge case?
    • SkyWarrior
    • December 02, 2020 05:52
    • Edited
    0 votes 8 comments
  • SVDiscovery OutOfMemoryError.
    • latte kim
    • December 01, 2020 07:56
    0 votes 5 comments
  • -DepthOfCoverage-ct not working in GATK 4.1.8.1
    • Wei
    • November 30, 2020 23:00
    0 votes 5 comments
  • No results of CollectvariantCallingMetrics Answered
    • Yenan
    • November 30, 2020 07:13
    0 votes 30 comments
  • how to set the minimum percentage of detectable mutation
    • Safa.J
    • November 27, 2020 20:37
    0 votes 0 comments
  • How do I rename output folder created using glob (WDL-Cromwell)?
    • Mar Quiroga
    • November 25, 2020 23:20
    1 vote 1 comment
  • How to use Directory type as defined in WDL development spec
    • Matthew Galvin
    • November 25, 2020 21:07
    0 votes 1 comment
  • CalculateContamination Sample Source
    • gufran
    • November 25, 2020 15:30
    • Edited
    0 votes 1 comment
  • MarkDuplicates has different duplication metrics than EstimateLibraryComplexity
    • Ravi Mandla
    • November 21, 2020 01:09
    0 votes 1 comment
  • CNNScoreVariants error: AttributeError: 'str' object has no attribute 'decode'
    • WKaiser
    • November 19, 2020 10:23
    • Edited
    0 votes 9 comments
  • Truncated bam file after running ReplaceSamHeader(Picard) Answered
    • kostas alexiou
    • November 17, 2020 15:12
    0 votes 6 comments
  • PathSeq Generate K-mer Library
    • DeLuca Lab
    • November 16, 2020 16:46
    0 votes 3 comments
  • ValidateSamFile: New error after running BQSR
    • ISmolicz
    • November 16, 2020 15:21
    0 votes 19 comments
  • MitochondriaPipeline on merged Bams
    • Valentin
    • November 12, 2020 11:05
    0 votes 4 comments
  • Rename sample in vcd.idx file
    • Vilde Bruhn
    • November 12, 2020 10:15
    0 votes 1 comment
  • IlluminaBasecallsToSam: How do I specify one unique RGID per output uBAM?
    • ISmolicz
    • November 09, 2020 14:14
    0 votes 8 comments
  • Resource bundle error download
    • Linda Do
    • November 05, 2020 18:09
    • Edited
    0 votes 7 comments
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