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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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  • Base Recalibrator " No Positional Argument is defined for this tool"
    • megha thippanna
    • January 27, 2023 05:40
    0 votes 0 comments
  • ApplyVQSR: "[W::bgzf_read_block] EOF marker is absent" and "[tabix] the index file exists." errors
    • Bob Ye
    • January 25, 2023 23:12
    0 votes 0 comments
  • Liftover Picard hg19 to hg38: variants were not successfully lifted over
    • Andres Caballero
    • December 09, 2022 18:39
    2 votes 2 comments
  • gatk4-GenotypeGVCFs.nf doens't recognize Primary_000001F chromosomes for process GatherVcfs
    • Carole Couture
    • December 08, 2022 15:19
    0 votes 0 comments
  • HaplotypeCaller confuses introns as long deletions
    • Vladimir Souza
    • November 09, 2022 23:03
    • Edited
    0 votes 3 comments
  • error when running ASEReadCounter
    • behzad
    • October 27, 2022 11:20
    0 votes 2 comments
  • SortSam - Question about I/O error
    • Henry
    • October 27, 2022 08:20
    0 votes 2 comments
  • Does GATK4 BaseRecalibrator not understand relative paths?
    • Eva (Evander)
    • October 17, 2022 12:51
    0 votes 10 comments
  • CombineGVCFs - possible to restart/continue run?
    • medgen
    • October 11, 2022 14:01
    0 votes 5 comments
  • CGA3_WES_Characterization_Pipeline_v0.2_Jun2019 PoN Errors...
    • Rose Gold
    • September 28, 2022 14:32
    0 votes 1 comment
  • GenomeSTRiP SVPreprocess error
    • Jibin Jeong
    • September 15, 2022 04:51
    • Edited
    1 vote 1 comment
  • Genomestrip: Argument with name '--ploidyMapFile' (-ploidyMapFile) is missing
    • Senwei
    • April 27, 2022 07:59
    1 vote 2 comments
  • Cromwell metadata of huge workflows
    • Rafal Gumienny
    • April 07, 2022 12:24
    • Edited
    0 votes 1 comment
  • Genomestrip preprocessing error
    • chae chae
    • March 08, 2022 03:41
    • Edited
    0 votes 13 comments
  • change the memory when running SVPreprocess
    • zzq
    • January 11, 2022 06:21
    • Edited
    0 votes 2 comments
  • VariantsToTable positional argument eror
    • Owen Hudson
    • December 14, 2021 17:22
    0 votes 1 comment
  • Dictionary cannot have size zero error
    • Nish314
    • November 20, 2021 00:20
    • Edited
    0 votes 1 comment
  • CNNScoreVariants carshes with java.lang.NullPointerException with Python 3.8 & JDK 1.8
    • KUMAR Chandan * TCS
    • November 02, 2021 09:56
    0 votes 1 comment
  • CalculateContamination 4.1.2.0 org.apache.commons.math3.exception.TooManyEvaluationsException
    • 陈星瀚
    • October 29, 2021 09:21
    0 votes 1 comment
  • HaplotypeCaller inconsistency with different interval lists
    • Gytis Mackevičius
    • September 10, 2021 05:53
    • Edited
    0 votes 5 comments
  • My recalibration table from BaseRecalibrator is empty
    • Calum Tattersfield
    • August 25, 2021 18:14
    • Edited
    0 votes 5 comments
  • SplitNCigarReads does not seem to split reads properly as it was before 3.8-1?
    • SkyWarrior
    • June 21, 2021 13:29
    • Edited
    0 votes 7 comments
  • Running Genome STRiP SVPreprocess, but I got error message: "Invalid command line: Malformed walker argument: Could not find walker with name: ComputeInsertSizeHistogramsWalker"
    • Norio Tanaka
    • June 15, 2021 14:22
    0 votes 4 comments
  • GenomicsDBImport - A USER ERROR has occurred: Failed to create reader from file: 2.0
    • Jared Johnson
    • May 07, 2021 20:44
    0 votes 1 comment
  • sample_gender.report.txt is empty when running SVpreprocess restricted to chromosomes
    • zzq
    • April 16, 2021 11:52
    • Edited
    0 votes 8 comments
  • How do I keep a glob from copying a file in Cromwell / WDL
    • Gregory Dougherty
    • March 09, 2021 00:24
    0 votes 1 comment
  • How to Fix the follow ValidateSamFile error ?
    • Luis Enrique Romero Cruz
    • March 06, 2021 03:51
    0 votes 1 comment
  • BaseRecalibrator on MT .bam files
    • Sharon Cox
    • February 19, 2021 09:48
    • Edited
    0 votes 1 comment
  • LiftoverVcf: hg19 to hg38 all variants mismatched
    • Ken Hanscombe
    • February 17, 2021 14:13
    0 votes 3 comments
  • Error when trying to generate the second recalibration table for AnalyzeCovariates
    • ISmolicz
    • February 17, 2021 12:03
    0 votes 10 comments
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