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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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  • GATK CNV somatic panels of normal design Answered
    • Mallika Gandham
    • May 04, 2022 16:07
    0 votes 3 comments
  • What does RAW_MQ annotation mean ?
    • Robert Baldwin
    • July 27, 2022 19:49
    0 votes 1 comment
  • SamToFastq - bam order
    • Jakub Savara
    • July 24, 2022 10:48
    0 votes 2 comments
  • Picard CollectHsMetrics output
    • Giovanni Cerchia
    • July 21, 2022 12:29
    0 votes 1 comment
  • Mitochondrial shifted reference Answered
    • MARC TORMO PUIGGROS
    • January 26, 2022 10:57
    0 votes 4 comments
  • Limit core use of DetermineGermlineContigPloidy & GermlineCNVCaller Answered
    • Blaz Vrhovsek
    • June 30, 2022 11:27
    1 vote 1 comment
  • HaplotypeCaller using one sample split in two bam files
    • elena vigorito
    • June 28, 2022 09:16
    0 votes 1 comment
  • GATK genomicsDBImport error Answered
    • @OK
    • June 14, 2022 11:11
    0 votes 3 comments
  • Documentation for running GATK and Cromwell on IBM Cloud Answered
    • Takeshi Yoshimura
    • April 05, 2022 01:24
    1 vote 7 comments
  • germline mutation calling using per-sample module
    • chenglei
    • June 08, 2022 16:06
    0 votes 1 comment
  • Haplotypecaller Answered
    • Mahdi Ahmadi
    • May 30, 2022 16:45
    0 votes 1 comment
  • JointGermlineCNVSegmentation Answered
    • Yangyxt
    • April 30, 2022 06:56
    0 votes 2 comments
  • BaseRecalibrator --max-cycle Answered
    • oğuzhan karaosmanoğlu
    • May 12, 2022 11:11
    0 votes 1 comment
  • Question on Java version Answered
    • Anand
    • May 10, 2022 15:24
    0 votes 2 comments
  • GetPileupSummaries common germline variant sites VCF hg38 Answered
    • Anish K
    • April 18, 2022 16:48
    0 votes 2 comments
  • MergeBamAlignment for mitochondrial variant discovery Answered
    • Ahmed S. Chakroun
    • March 18, 2022 17:33
    0 votes 1 comment
  • how to run "gatk-register"? Answered
    • Mahendra Singh
    • March 28, 2022 04:28
    0 votes 2 comments
  • MergeBamAlignment conflicting headers between mapped and unmapped Answered
    • TA
    • March 04, 2022 15:13
    0 votes 3 comments
  • Is FilterAlignmentArtifacts out of the Mutect2 calling best practices? Answered
    • shenglai
    • March 11, 2022 01:53
    0 votes 1 comment
  • Single sample germline - VQSR+CNN or just CNN
    • Jordan Russell
    • March 18, 2022 15:45
    0 votes 5 comments
  • genotyping calls don't align with coverage Answered
    • Gertjan Wils
    • March 15, 2022 12:57
    1 vote 1 comment
  • How is tumor_f in Funcotator MAF Answered
    • Robert Bremel
    • May 26, 2020 17:11
    0 votes 3 comments
  • VariantsToTable not working Answered
    • Arwa Ahmad
    • February 25, 2022 08:56
    0 votes 2 comments
  • How to evlauate the result: GenotypeConcordance or Concordance Answered
    • lizhichao
    • February 17, 2022 09:09
    0 votes 6 comments
  • GATK GenotypeGVCFs miss a real Insertion Answered
    • touyupang
    • February 18, 2022 07:45
    0 votes 6 comments
  • Values for QD annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations.
    • tahi
    • February 22, 2022 08:48
    0 votes 1 comment
  • Genomes in the cloud docker file
    • J LoPiccolo
    • February 23, 2022 16:38
    0 votes 0 comments
  • germline-resource Answered
    • Juechen Yang
    • March 17, 2020 17:32
    0 votes 10 comments
  • Mosaic gCNVs with GATK Answered
    • Naga
    • January 13, 2022 17:32
    • Edited
    0 votes 1 comment
  • WDL pipeline: Mitochondrial-short-variant-discovery Answered
    • manolis
    • January 25, 2022 07:57
    0 votes 2 comments
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