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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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Show all All Planned Not planned Completed Answered No status Sort by comments Newest post Recent activity Votes Comments
  • Loss of data after HaplotypeCaller
    • mbesskd5
    • February 14, 2020 10:14
    • Edited
    0 votes 5 comments
  • ShiftFasta creates empty intervals file Answered
    • Ram
    • October 21, 2022 07:56
    • Edited
    0 votes 4 comments
  • How can I build the GATK jar so that the intel native libraries are available? Answered
    • Mark Schreiber
    • September 22, 2022 16:49
    0 votes 4 comments
  • libgkl_compression.so not found + Failed to detect Google Compute Engine in a GATK workflow Answered
    • Marta Giovalli
    • September 14, 2022 12:47
    • Edited
    0 votes 4 comments
  • Haploytpe caller shows me that 0 read(s) were filtered by: MappingQualityAvailableReadFilter etc. Answered
    • pb
    • July 13, 2022 14:15
    0 votes 4 comments
  • Refseq accession number and version number in Funcotator Answered
    • TMB
    • April 26, 2022 04:13
    0 votes 4 comments
  • vulnerability issue for gatk-package-4.2.5.0-local.jar Answered
    • John Yu
    • March 09, 2022 14:27
    0 votes 4 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
  • How to merge approx 150 bam file using Picard
    • Abrish
    • December 27, 2020 14:02
    0 votes 4 comments
  • DepthOfCoverage in GATK4.1.9.0 with -gene-list option
    • David Jaspez
    • December 21, 2020 17:36
    • Edited
    0 votes 4 comments
  • MitochondriaPipeline on merged Bams
    • Valentin
    • November 12, 2020 11:05
    0 votes 4 comments
  • Interval Filtering -- How does it actually work?
    • Alijah O'Connor
    • September 21, 2020 22:54
    • Edited
    0 votes 4 comments
  • Picard LiftOverVCF 2.22.3. hs37d5_to_GRCh38. Many mismatched reference alleles
    • Argonaut44
    • June 23, 2020 18:09
    • Edited
    0 votes 4 comments
  • Picard CollectHsMetrics PCT_EXC_OFF_TARGET
    • Holly Corbitt
    • May 07, 2020 04:09
    1 vote 4 comments
  • A USER ERROR has occurred: Number of read groups must be >= 1, but is 0
    • Jay Singh
    • May 01, 2020 17:24
    0 votes 4 comments
  • Do I need to perform fastqc and adapters trimming before gatk pipeline?
    • LG
    • May 01, 2020 02:49
    2 votes 4 comments
  • ValidateSamFile tmp not found ERROR with not output or Exception
    • James
    • April 20, 2020 23:34
    0 votes 4 comments
  • Picard ExtractIlluminaBarcodes return NullPointerException error
    • Jing Lin
    • March 20, 2020 21:52
    0 votes 4 comments
  • Do BQSR ignore VCF sites marked as filtered, or must they be removed from the file?
    • mk
    • March 11, 2020 00:37
    0 votes 4 comments
  • Question: Picard - MergeBamAlignment: Reads remaining on alignment iterator
    • Nguyen Nguyen Thanh
    • February 23, 2020 15:03
    0 votes 4 comments
  • HaplotypeCaller produces very large .idx files
    • Anze Staric
    • February 20, 2020 20:30
    1 vote 4 comments
  • WES covarage analysis
    • Surdan Burasi
    • February 16, 2020 21:09
    0 votes 4 comments
  • HaplotypeCaller confuses introns as long deletions
    • Vladimir Souza
    • November 09, 2022 23:03
    • Edited
    0 votes 3 comments
  • Error in Running command CreateExtendedIlluminaManifest Answered
    • Nur Adlina Binti Mohd Affian
    • October 03, 2022 09:21
    0 votes 3 comments
  • How to run muTect without normal sample? Answered
    • Yingjie Zhu
    • July 11, 2022 21:35
    1 vote 3 comments
  • markDuplicatesSpark running out of memory Answered
    • Matt Snyder
    • June 09, 2022 19:34
    0 votes 3 comments
  • GATK R plots with R v4.1.2 Answered
    • Franz Gassner
    • January 24, 2022 09:36
    0 votes 3 comments
  • markduplicatesSpark .bam.parts output error (directory already exists) Answered
    • Morgan Sparks
    • September 30, 2021 16:31
    0 votes 3 comments
  • GenomeSTRiP SVPreprocess failed Answered
    • Jenny Xu
    • July 27, 2021 02:46
    0 votes 3 comments
  • LiftoverVcf: hg19 to hg38 all variants mismatched
    • Ken Hanscombe
    • February 17, 2021 14:13
    0 votes 3 comments
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