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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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  • Steps For GATK-gCNV pipleline on Exome Data
    • Y R
    • April 03, 2023 15:30
    • Edited
    0 votes 12 comments
  • ApplyBQSR
    • Wondessen Ayalew
    • February 23, 2023 06:19
    0 votes 10 comments
  • VCF file SNP ID missing
    • Wondessen Ayalew
    • June 29, 2023 08:48
    • Edited
    0 votes 9 comments
  • DP for each variant bulk is skewed towards 50 and multiples of 50
    • Lauren Fedenia
    • April 21, 2021 19:02
    0 votes 7 comments
  • CollectInsertSizeMetrics can't find R
    • Craig Amundsen
    • July 21, 2023 22:15
    0 votes 6 comments
  • GATK MarkDuplicates Missing output file
    • Gilgamesh
    • August 30, 2023 17:35
    1 vote 5 comments
  • GATK configration
    • Wondessen Ayalew
    • February 13, 2023 12:28
    0 votes 5 comments
  • Markduplicates
    • Atal Saha
    • January 03, 2023 16:55
    0 votes 5 comments
  • Estimate genotype proportions from filtered variants
    • Daniel Castañeda Mogollón
    • April 05, 2022 05:49
    0 votes 5 comments
  • Running best practices workflow step-by-step in command line
    • limetree
    • June 04, 2021 05:12
    1 vote 5 comments
  • How to provide custom exon-intron annotation source in Funcotator
    • Elisabetta Manduchi
    • February 18, 2022 13:48
    0 votes 4 comments
  • GATK4.0.3.0 - CombineGVCFs - Unexpected base in allele bases
    • HT
    • October 01, 2021 05:28
    0 votes 4 comments
  • Issue with Running MuTect in GATK Version Compatibility
    • 김수영
    • August 31, 2023 06:44
    0 votes 3 comments
  • cnv_germline_case_workflow.wdl
    • Sheryl
    • August 23, 2023 05:10
    0 votes 3 comments
  • PICARD/Gradle build fail
    • Olivia Cheng
    • June 28, 2023 22:52
    0 votes 3 comments
  • Mutect2 wdl interval list and scatter count
    • Sheryl
    • March 06, 2023 02:19
    • Edited
    0 votes 3 comments
  • Help with running GATK RNAseq workflow with docker backend and multiple cpus?
    • ThyagoLC
    • September 02, 2021 15:38
    • Edited
    0 votes 3 comments
  • get the basics for Haplotypecaller
    • Maarten Nijenhuis
    • June 02, 2023 10:37
    0 votes 2 comments
  • Is It Allowed To Submit An Entire Code For Review?
    • Y R
    • April 23, 2023 10:09
    0 votes 2 comments
  • Interval list and the “Mate not found” error in WES data
    • LY Wang
    • April 07, 2023 13:19
    0 votes 2 comments
  • Is there a way to preserve numeric genotypes with VariantsToTable?
    • Ben Sprung
    • January 11, 2023 18:16
    0 votes 2 comments
  • Scatter Gather principle by chromosome on Gatk
    • Sushant Sawant
    • November 28, 2022 06:44
    • Edited
    1 vote 2 comments
  • Where can I download Homo_sapiens_assembly38.haplotype_database.txt
    • Sheryl
    • November 17, 2022 05:36
    0 votes 2 comments
  • Mutect2 somatic mutation calling for plant
    • Lina Herliana
    • September 15, 2021 01:42
    0 votes 2 comments
  • Scatter / Gather for BaseRecalibrator on a single human WES dataset
    • asg
    • January 30, 2020 07:48
    • Edited
    0 votes 2 comments
  • GATK-SV HPC VM hardware requirements
    • Georgia Hosking
    • August 14, 2023 07:18
    • Edited
    0 votes 1 comment
  • Mitochondrial pipeline requirement
    • Sheryl
    • June 15, 2023 01:55
    0 votes 1 comment
  • ExomeSingleSample wdl
    • Sheryl
    • June 08, 2023 02:07
    0 votes 1 comment
  • STAR and GATK RNAseq based SNP detection
    • Jahn Davik
    • May 03, 2023 08:14
    0 votes 1 comment
  • Best practice with read groups
    • Sheryl
    • April 27, 2023 00:43
    0 votes 1 comment
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