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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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  • ASEReadCounter java.lang.ArrayIndexOutOfBoundsException: 0
    • zhaol
    • January 08, 2021 07:38
    0 votes 3 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
  • Clarity on Variant Callers being "optimized for UMI-containing data"
    • Alijah O'Connor
    • December 18, 2020 00:49
    • Edited
    0 votes 1 comment
  • How do I get intermediate outputs from cromwell
    • Matthias De Smet
    • December 15, 2020 09:59
    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
  • How to merge approx 150 bam file using Picard
    • Abrish
    • December 27, 2020 14:02
    0 votes 4 comments
  • BQSR no output table found
    • Tamrin Chowdhury
    • December 17, 2020 07:20
    0 votes 3 comments
  • Missing ReadPosRankSum, MQRankSum and BaseQRankSum Scores in VCF
    • Hamza Umut Karakurt
    • December 14, 2020 08:33
    0 votes 1 comment
  • SVDiscovery OutOfMemoryError.
    • latte kim
    • December 01, 2020 07:56
    0 votes 5 comments
  • MarkDuplicatesSpark crash
    • David Gómez-Sánchez
    • January 07, 2020 17:02
    1 vote 9 comments
  • Errors with CNNScoreVariants and HaplotypeCaller: java.nio.BufferUnderflowException
    • WKaiser
    • December 03, 2020 16:11
    0 votes 3 comments
  • Error in SplitNCigarReads
    • Giulia Corsi
    • August 19, 2020 15:26
    0 votes 11 comments
  • -DepthOfCoverage-ct not working in GATK 4.1.8.1
    • Wei
    • November 30, 2020 23:00
    0 votes 5 comments
  • Some stop positions of .interval_list is smaller than the start positions
    • Shiva Kazempour
    • December 02, 2020 15:35
    0 votes 2 comments
  • ValidateSamFile: New error after running BQSR
    • ISmolicz
    • November 16, 2020 15:21
    0 votes 19 comments
  • options used during base recalibration
    • janick mathys
    • January 30, 2020 12:36
    0 votes 6 comments
  • How do I rename output folder created using glob (WDL-Cromwell)?
    • Mar Quiroga
    • November 25, 2020 23:20
    1 vote 1 comment
  • CalculateContamination Sample Source
    • gufran
    • November 25, 2020 15:30
    • Edited
    0 votes 1 comment
  • How to use Directory type as defined in WDL development spec
    • Matthew Galvin
    • November 25, 2020 21:07
    0 votes 1 comment
  • how to set the minimum percentage of detectable mutation
    • Safa.J
    • November 27, 2020 20:37
    0 votes 0 comments
  • MarkDuplicates has different duplication metrics than EstimateLibraryComplexity
    • Ravi Mandla
    • November 21, 2020 01:09
    0 votes 1 comment
  • PathSeq Generate K-mer Library
    • DeLuca Lab
    • November 16, 2020 16:46
    0 votes 3 comments
  • Error running FilterMutectCalls: alpha must be greater than 0 but got NaN
    • Larry S
    • September 20, 2020 14:48
    0 votes 13 comments
  • MitochondriaPipeline on merged Bams
    • Valentin
    • November 12, 2020 11:05
    0 votes 4 comments
  • IlluminaBasecallsToSam: How do I specify one unique RGID per output uBAM?
    • ISmolicz
    • November 09, 2020 14:14
    0 votes 8 comments
  • error in GATK mitochondria pipeline
    • CenLiau
    • August 12, 2020 21:23
    0 votes 7 comments
  • Rename sample in vcd.idx file
    • Vilde Bruhn
    • November 12, 2020 10:15
    0 votes 1 comment
  • Clear missing variant from HaplotypeCaller
    • Edu Andrés León
    • October 15, 2020 10:26
    • Edited
    0 votes 9 comments
  • Read groups: How do I assign RGID when all samples in a pool are run on all available lanes on a flow cell?
    • ISmolicz
    • November 03, 2020 11:45
    0 votes 2 comments
  • GenomicsDBImport running out of memory?
    • Ivan
    • October 28, 2020 11:14
    0 votes 8 comments
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