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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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  • Genome STRiP CNVDiscovery pipeline error
    • Beilei Bian
    • March 25, 2020 00:39
    0 votes 27 comments
  • ValidateSamFile: New error after running BQSR
    • ISmolicz
    • November 16, 2020 15:21
    0 votes 19 comments
  • How to run GenotypeConcordance
    • Ana Marija
    • September 12, 2020 00:57
    • Edited
    0 votes 19 comments
  • Problem Installing GATK python environment - SOLUTION POSTED! Featured
    • SkyWarrior
    • February 06, 2020 07:21
    • Edited
    1 vote 17 comments
  • filterSamReads stdout format error
    • rcorbett
    • February 04, 2021 15:31
    • Edited
    0 votes 15 comments
  • ERROR MESSAGE: No gender data for sample:sample7
    • termius
    • August 05, 2020 07:02
    0 votes 15 comments
  • Fatal error occuring during GATK4 PathSeqPipeline tool run
    • Jude Taylor
    • July 14, 2020 12:40
    0 votes 15 comments
  • MarkDuplicatesSparks not removing some duplicates?
    • Tom Morrison
    • June 18, 2020 14:55
    0 votes 15 comments
  • Setting SPARK resources when using the gatk release version
    • Ury Alon
    • May 18, 2020 04:42
    • Edited
    0 votes 15 comments
  • Broken: conda env create -n gatk -f gatkcondaenv.yml
    • James White
    • April 24, 2020 17:01
    0 votes 15 comments
  • Genomestrip preprocessing error
    • chae chae
    • March 08, 2022 03:41
    • Edited
    0 votes 13 comments
  • Error running FilterMutectCalls: alpha must be greater than 0 but got NaN
    • Larry S
    • September 20, 2020 14:48
    0 votes 13 comments
  • Any automatic downloadable gatk3?
    • ale
    • January 09, 2020 13:16
    2 votes 13 comments
  • mitochondria_m2_wdl: MitochondriaPipeline Issues
    • Valentin
    • July 09, 2020 13:42
    0 votes 12 comments
  • GATK4 HaplotypeCaller ERROR : expected haplotypes.size() >= eventsAtThisLoc.size() + 1
    • Şevval Aktürk
    • April 23, 2020 12:26
    0 votes 12 comments
  • Error in SplitNCigarReads
    • Giulia Corsi
    • August 19, 2020 15:26
    0 votes 11 comments
  • Merge different individual VCF
    • Linda Do
    • July 06, 2020 07:05
    1 vote 11 comments
  • FilterByOrientationBias vanished in 4.1.6.0
    • riederd
    • March 30, 2020 11:41
    0 votes 11 comments
  • Error when trying to generate the second recalibration table for AnalyzeCovariates
    • ISmolicz
    • February 17, 2021 12:03
    0 votes 10 comments
  • FixVcfHeader error: A reference dictionary is required for creating Tribble indices on the fly
    • jorgez
    • July 20, 2020 18:52
    0 votes 10 comments
  • LiftoverVcf fails to lift over a GVCF file. Error java.lang.ArrayIndexOutOfBoundsException: -1
    • jorgez
    • May 06, 2020 12:54
    0 votes 10 comments
  • HaplotypeCaller complains (in 2 different ways) about sample-name
    • Terry Jones
    • February 18, 2020 14:07
    0 votes 10 comments
  • CNNScoreVariants error: AttributeError: 'str' object has no attribute 'decode'
    • WKaiser
    • November 19, 2020 10:23
    • Edited
    0 votes 9 comments
  • Clear missing variant from HaplotypeCaller
    • Edu Andrés León
    • October 15, 2020 10:26
    • Edited
    0 votes 9 comments
  • Genomestrip cannot find --ploidyMapFile
    • Swanthana Rekulapally
    • June 11, 2020 20:23
    0 votes 9 comments
  • Recal file with malformed header
    • Erik Fasterius
    • May 14, 2020 09:43
    0 votes 9 comments
  • GenotypeGVCFs: java.lang.NullPointerException
    • Anze Staric
    • March 30, 2020 11:28
    0 votes 9 comments
  • MarkDuplicatesSpark crash
    • David Gómez-Sánchez
    • January 07, 2020 17:02
    1 vote 9 comments
  • sample_gender.report.txt is empty when running SVpreprocess restricted to chromosomes
    • zzq
    • April 16, 2021 11:52
    • Edited
    0 votes 8 comments
  • GermlineCNVCaller edge case?
    • SkyWarrior
    • December 02, 2020 05:52
    • Edited
    0 votes 8 comments
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