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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 1 comment
  • 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 1 comment
  • 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
  • Picard CollectHsMetrics PCT_TARGET_BASES Output
    • michaelmc
    • February 23, 2023 17:04
    0 votes 2 comments
  • error:Argument --emit-ref-confidence
    • Rezwan Tariq
    • February 22, 2023 10:09
    0 votes 0 comments
  • Funcotator 4.1.2.0 gencode for locatableXSV
    • Frank Maiwald
    • February 20, 2023 11:55
    0 votes 1 comment
  • Intervals and GenomicsDBImport
    • Irbin Manuel Veliz Isidro
    • February 17, 2023 09:35
    0 votes 2 comments
  • How does Mutect2 count read depth/coverage? Answered
    • Sameer Shankar
    • February 16, 2023 20:40
    1 vote 11 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
  • 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
  • Best practice trios
    • Sheryl
    • November 23, 2022 00:58
    • Edited
    0 votes 0 comments
  • BuildBamIndex
    • Robert Bremel
    • November 08, 2022 20:27
    0 votes 4 comments
  • Report file CreateExtendedIlluminaManifest Report file
    • James Gallant
    • October 31, 2022 15:28
    1 vote 1 comment
  • 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
  • Can't access google cloud it says permission required
    • HQ Zhao
    • October 27, 2022 02:03
    0 votes 2 comments
  • 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
  • Mutect2 produces 0 results for somatic mutation calling of paired-end reads (BAM)
    • Di Pan
    • October 09, 2022 05:22
    • Edited
    0 votes 1 comment
  • Issues with LiftoverVcf Answered
    • Mohammad Deen Hayatu
    • October 06, 2022 06:43
    0 votes 6 comments
  • Documentation for interval files in resource bundle
    • Laura Egolf
    • September 19, 2022 21:28
    0 votes 1 comment
  • UmiAwareMarkDuplicatesWithMateCigar - UMI_METRICS
    • Miguel Grau
    • September 13, 2022 10:55
    • Edited
    0 votes 2 comments
  • CalculateFingerprintMetrics Usability On Somatic Samples
    • Kathryn Kananen
    • September 13, 2022 04:16
    • Edited
    0 votes 1 comment
  • Request: examples of svtk usage
    • Yaping Wu
    • September 10, 2022 01:30
    0 votes 1 comment
  • Too many duplicate articles Answered
    • Дмитрий Голик
    • September 09, 2022 09:14
    0 votes 2 comments
  • ASEReadCount Only Outputting the First Chromosome Answered
    • Leslie Youtsey
    • August 31, 2022 19:31
    0 votes 3 comments
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