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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 votes Newest post Recent activity Votes Comments
  • GenomeSTRiP SVGenotyper not producing genotypes
    • Laura Cottino
    • September 25, 2020 11:48
    0 votes 2 comments
  • Error running FilterMutectCalls: alpha must be greater than 0 but got NaN
    • Larry S
    • September 20, 2020 14:48
    0 votes 13 comments
  • Interval Filtering -- How does it actually work?
    • Alijah O'Connor
    • September 21, 2020 22:54
    • Edited
    0 votes 4 comments
  • error while running gatk GenotypeConcordance
    • Ana Marija
    • September 16, 2020 17:04
    0 votes 2 comments
  • How to run GenotypeConcordance
    • Ana Marija
    • September 12, 2020 00:57
    • Edited
    0 votes 19 comments
  • Threads parameters of Depth of coverage (GATK4.1.7.0 beta version)
    • Henry
    • September 11, 2020 06:16
    • Edited
    0 votes 1 comment
  • FuncotatorDataSourceDownloader does not download latest version?
    • A. Brink
    • September 10, 2020 13:50
    0 votes 1 comment
  • Weird parameter of Depth of coverage (GATK4.1.7.0 beta version)
    • Henry
    • September 11, 2020 06:05
    • Edited
    0 votes 1 comment
  • Where and how I can get GenomeAnalysisTK.jar script?
    • Ana Marija
    • September 04, 2020 22:35
    0 votes 1 comment
  • gatk-4.1.8.1/ValidateVariants - bypass contig length check?
    • Matthew Maher
    • September 03, 2020 15:44
    0 votes 1 comment
  • Error on FastaAlternateReferenceMaker process
    • JaeJun Lee
    • September 03, 2020 06:09
    0 votes 1 comment
  • CompareSams with LENIENT_HEADER=true doesn't work
    • Uri David Akavia
    • September 01, 2020 20:11
    0 votes 2 comments
  • CombineVariants set attribute filters on all callers explicitly (not with filteredInAll)
    • jorgez
    • September 01, 2020 11:41
    0 votes 1 comment
  • GenotypeGVCFs stops halfway through scaffold - java.lang.NullPointerException
    • Peter Euclide
    • August 29, 2020 14:16
    0 votes 1 comment
  • Error in running SplitNCigarReads - htsjdk.samtools.util.RuntimeIOException Answered
    • KATHIE NGO
    • August 27, 2020 17:31
    • Edited
    0 votes 8 comments
  • HaplotypeCaller produces variant lines with no depth information when calling gvcf
    • Berk Gonenc
    • August 22, 2020 14:27
    0 votes 1 comment
  • Error in SplitNCigarReads
    • Giulia Corsi
    • August 19, 2020 15:26
    0 votes 11 comments
  • PathSeq output
    • Arman Ardalan
    • August 18, 2020 07:49
    0 votes 3 comments
  • Workshop materials
    • Wolfgang Resch
    • August 17, 2020 20:35
    0 votes 2 comments
  • error in GATK mitochondria pipeline
    • CenLiau
    • August 12, 2020 21:23
    0 votes 7 comments
  • How to make a 1kg_ref_panel_v1.ped?
    • 2tong
    • August 11, 2020 02:09
    • Edited
    0 votes 1 comment
  • --tmp-dir option user error Answered
    • Brynjar Sigurðsson
    • August 10, 2020 12:22
    0 votes 13 comments
  • Discord / Slack group
    • Saatvig Patel
    • August 05, 2020 16:39
    0 votes 1 comment
  • ERROR MESSAGE: No gender data for sample:sample7
    • termius
    • August 05, 2020 07:02
    0 votes 15 comments
  • Error: Invalid or corrupt jarfile cromwell-52.jar
    • Saatvig Patel
    • July 27, 2020 10:07
    0 votes 3 comments
  • Speeding up GATK4 DepthOfCoverage
    • Michael Franklin
    • July 27, 2020 02:11
    0 votes 2 comments
  • SelectVariants error
    • Rajul Tayal
    • July 25, 2020 09:12
    • Edited
    0 votes 1 comment
  • Dosages with Mutect2
    • Leore Nehemie Bensabath
    • July 24, 2020 08:36
    0 votes 6 comments
  • GATK mark duplicates error
    • Kshama Aswath
    • July 22, 2020 20:26
    • Edited
    0 votes 2 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
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