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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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  • is --dont-use-soft-clipped-bases discarded in HaplotypeCaller?
    • Songming Liu
    • March 24, 2023 07:45
    0 votes 0 comments
  • Genotype filtering still write "PASS" in filter field
    • Marissa Eronika
    • March 21, 2023 15:50
    1 vote 0 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 0 comments
  • How does Mutect2 count read depth/coverage? Answered
    • Sameer Shankar
    • February 16, 2023 20:40
    1 vote 11 comments
  • Using haplotype information from high-coverage samples as a prior for Haplotypecaller for other low-coverage samples in the same dataset?
    • Nils Paffen
    • March 07, 2023 16:43
    0 votes 1 comment
  • Intervals and GenomicsDBImport
    • Irbin Manuel Veliz Isidro
    • February 17, 2023 09:35
    0 votes 2 comments
  • Picard CollectHsMetrics PCT_TARGET_BASES Output
    • michaelmc
    • February 23, 2023 17:04
    0 votes 2 comments
  • Funcotator 4.1.2.0 gencode for locatableXSV
    • Frank Maiwald
    • February 20, 2023 11:55
    0 votes 1 comment
  • error:Argument --emit-ref-confidence
    • Rezwan Tariq
    • February 22, 2023 10:09
    0 votes 0 comments
  • CallCopyRatioSegments -- how does it work? Answered
    • Austin Southard-Smith
    • February 10, 2023 20:46
    0 votes 3 comments
  • gatk SelectVariant identified no snps in the vsf file while it has 63702926 snps
    • Vishal Negi
    • February 06, 2023 19:24
    0 votes 1 comment
  • Why don't I have access to some links? Answered
    • Manuel
    • January 12, 2022 11:13
    0 votes 3 comments
  • GATK Mutect2 tumor vs. normal sample Answered
    • Enrico Cocchi
    • October 02, 2020 16:23
    0 votes 4 comments
  • Variables harmonization tutorial for variables collected from Pic-sure from various cohort
    • kei_hang_chan
    • January 26, 2023 06:18
    0 votes 0 comments
  • Picard's CollectRnaSeqMetrics
    • Benli Chai
    • January 17, 2023 20:36
    0 votes 0 comments
  • Detailed reason for filtering by FilterMutectCalls
    • tan qiang
    • January 13, 2023 07:44
    0 votes 0 comments
  • How to specify number of threads while running Mutect2
    • Tanay Biswas
    • December 21, 2022 05:49
    0 votes 0 comments
  • Should we run MarkDuplicates on PCR-Free Libraries made using PCR-Free Kits to take care of Optical Duplicates ?
    • rohit satyam
    • July 28, 2020 20:28
    • Edited
    0 votes 3 comments
  • BuildBamIndex
    • Robert Bremel
    • November 08, 2022 20:27
    0 votes 4 comments
  • Best practice trios
    • Sheryl
    • November 23, 2022 00:58
    • Edited
    0 votes 0 comments
  • Java exception: index 65 is CONSTANT_MethodRef and should be CONSTANT_InterfaceMethodRef
    • Julián García-Abadillo
    • October 27, 2022 13:37
    • Edited
    0 votes 2 comments
  • vcf files for BQSR step Answered
    • Varun Gupta
    • March 30, 2020 22:13
    1 vote 4 comments
  • mutect2 multi-sample Answered
    • zhao shilin
    • May 07, 2020 17:27
    • Edited
    0 votes 35 comments
  • What does RAW_MQ annotation mean ?
    • Robert Baldwin
    • July 27, 2022 19:49
    0 votes 3 comments
  • Can't access google cloud it says permission required
    • HQ Zhao
    • October 27, 2022 02:03
    0 votes 2 comments
  • Report file CreateExtendedIlluminaManifest Report file
    • James Gallant
    • October 31, 2022 15:28
    1 vote 1 comment
  • RGID versus RGPU
    • Jean-Michel Carter
    • October 20, 2022 06:49
    • Edited
    0 votes 1 comment
  • Picard SortSam error Answered
    • Tanay Biswas
    • October 14, 2022 11:18
    0 votes 3 comments
  • Picard CollectHsMetrics output
    • Giovanni Cerchia
    • July 21, 2022 12:29
    0 votes 3 comments
  • Issues with LiftoverVcf Answered
    • Mohammad Deen Hayatu
    • October 06, 2022 06:43
    0 votes 6 comments
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