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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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Documentation Questions

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  • Select Variants
    • Patrick Bianchi
    • November 29, 2023 10:29
    0 votes 2 comments
  • GATK problem with the CombineGVCFs
    • David Sanchez Sotomayor
    • November 20, 2023 21:26
    0 votes 1 comment
  • How to use the --alleles option of HaplotypeCaller ?
    • Chloé Girard
    • November 10, 2023 16:58
    • Edited
    0 votes 8 comments
  • GATK Funcotator MAF header
    • Gregory Joseph
    • September 19, 2023 21:13
    0 votes 1 comment
  • Maximum number of Plasma samples by use mutect2 multi-sample pipeline
    • Jiao Zhang
    • September 20, 2023 01:50
    • Edited
    0 votes 2 comments
  • Missing documentation on somatic variant calling output VCF
    • Fia
    • October 22, 2023 20:55
    0 votes 1 comment
  • Picard MarkDuplicates Functionality
    • Nagashree Rachote
    • October 23, 2023 12:51
    0 votes 1 comment
  • MergeMutectStats missing from documentation
    • G E
    • October 20, 2023 02:01
    0 votes 1 comment
  • What is the recommended way to use/parse Funcotator output?
    • Steffen Møller Bøttger
    • October 11, 2023 10:52
    • Edited
    0 votes 1 comment
  • Extraction standards for SNP and INDEL
    • 子安 魏
    • August 25, 2023 09:47
    0 votes 1 comment
  • HaplotypeCaller dont call high supported variant
    • Filipe Dezordi
    • August 14, 2023 18:15
    0 votes 1 comment
  • Converting Reference Genomes from b37 to hg19
    • Abhi Agarwal
    • December 30, 2020 19:12
    0 votes 6 comments
  • Confusion regarding the Picard EstimateLibraryComplexity utility
    • Thomas Bradley
    • May 14, 2023 20:40
    • Edited
    0 votes 1 comment
  • gatk4.3.0.0 Combines gvcfs were interrupted without errors
    • dy lcc
    • June 26, 2023 06:57
    0 votes 2 comments
  • HOW TO EXCLUDE FILTERED VARIANTS WITH VARIANTFILTRATION?
    • Rômulo Carleial
    • July 07, 2023 12:46
    1 vote 1 comment
  • License / use terms for GATK resource bundle
    • Mariana E. M.
    • July 04, 2023 10:17
    1 vote 2 comments
  • How to prioritize EGFR transcript for annotation in Funcotator?
    • Bhavneet Bhinder
    • June 26, 2023 19:10
    0 votes 1 comment
  • Genomes in the cloud docker file
    • J LoPiccolo
    • February 23, 2022 16:38
    0 votes 2 comments
  • Cannot find explanation for odd vcf genotype format
    • David R
    • June 13, 2023 20:34
    0 votes 1 comment
  • What argument(s) should be used instead of --debug-graph-transformations?
    • ISmolicz
    • June 08, 2023 21:46
    • Edited
    0 votes 3 comments
  • How to Split 3000 WGS CRAM files into 1Mbp length chunks
    • Saeed Farajzadeh Valilou
    • May 24, 2023 15:30
    0 votes 1 comment
  • BOTHSIDES_SUPPORT filter in GATK-SV VCF
    • Matthew Hobbs
    • May 23, 2023 00:49
    0 votes 2 comments
  • How to find or generate common germline variant sites VCF required by GetPileupSummaries
    • Antti Koskenalho
    • May 27, 2020 06:22
    1 vote 4 comments
  • What is the purpose of TAGS_TO_DROP=MAX_AF when using RECOVER_SWAPPED_REF_ALT=true?
    • Peter Braund
    • May 12, 2023 13:09
    0 votes 2 comments
  • using the PlotDenoisedCopyRatios() function in gatk4
    • 泽 张
    • May 08, 2023 07:58
    0 votes 1 comment
  • CONVERT BAM TO U-BAM
    • Elin Mehrasa
    • April 27, 2023 23:17
    0 votes 1 comment
  • GATK-SV VCF interpretation
    • TejasJ
    • May 01, 2023 16:25
    0 votes 2 comments
  • Collecting chrM reads for mitochondrial analysis & MarkDuplicates
    • ana_snc
    • May 08, 2023 14:40
    • Edited
    0 votes 1 comment
  • Explanation on the HS Penalty metric
    • Pierre_Bioinfo
    • April 20, 2023 07:51
    1 vote 3 comments
  • Why is the coverage cut abruptly for a region in the bamout file of Mutect2 in comparison to the region in input files?
    • ISmolicz
    • March 21, 2023 00:15
    0 votes 5 comments
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