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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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  • GenomeSTRiP SVGenotyper not producing genotypes
    • Laura Cottino
    • September 25, 2020 11:48
    0 votes 2 comments
  • GATK asereadcounter for single cell data
    • Ben Strober
    • September 24, 2020 15:37
    0 votes 1 comment
  • 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
  • how to interpret results of gatk Concordance
    • Ana Marija
    • September 03, 2020 00:46
    0 votes 7 comments
  • ASEReadCounter count each read only once or not
    • Qingnan Liang
    • September 02, 2020 00:38
    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
  • Asereadcounter getting gene level count
    • hemant c naik
    • August 28, 2020 19:05
    0 votes 1 comment
  • Error in running SplitNCigarReads - htsjdk.samtools.util.RuntimeIOException
    • KATHIE NGO
    • August 27, 2020 17:31
    • Edited
    0 votes 6 comments
  • SplitNCigarReads merge reads together
    • Mic L
    • August 27, 2020 11:45
    0 votes 1 comment
  • VQSR in variants on X chromosome
    • Jaeyoon Chung
    • August 26, 2020 18:27
    1 vote 2 comments
  • HaplotypeCaller produces variant lines with no depth information when calling gvcf
    • Berk Gonenc
    • August 22, 2020 14:27
    0 votes 1 comment
  • Need help on variant filtration
    • DANSON WOOI
    • August 20, 2020 07:44
    0 votes 1 comment
  • error-handling-end-exit-codes-in-gatk
    • Kshama Aswath
    • August 19, 2020 18:50
    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
  • Using stdin with GATK
    • jodybk
    • August 12, 2020 14:07
    0 votes 1 comment
  • How to make a 1kg_ref_panel_v1.ped?
    • 2tong
    • August 11, 2020 02:09
    • Edited
    0 votes 1 comment
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