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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 no status All Planned Not planned Completed Answered No status Sort by comments Newest post Recent activity Votes 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
  • 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
  • Mutect2 wdl interval list and scatter count
    • Sheryl
    • March 06, 2023 02:19
    • Edited
    0 votes 3 comments
  • ApplyBQSR
    • Wondessen Ayalew
    • February 23, 2023 06:19
    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
  • 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
  • MarkDuplicatesSpark Error
    • Yosra Bejaoui
    • February 08, 2023 06:25
    0 votes 1 comment
  • Genotype and AD in Mutect2 vcf output
    • Ester Feldmesser
    • February 02, 2023 13:56
    0 votes 1 comment
  • VariantFiltration Issue
    • Ethan Mattice
    • January 04, 2023 17:57
    0 votes 1 comment
  • Multi-library designs: error proceeding from pre-processing to variant calling
    • Sabrina McNew
    • August 23, 2022 20:35
    0 votes 1 comment
  • GenomicsDB Import issues
    • aheritas
    • July 15, 2022 15:47
    0 votes 1 comment
  • Cromwell configuration problem: "No configuration setting found for key 'job-id-regex'"
    • Joel Wallenius
    • May 02, 2022 10:38
    0 votes 1 comment
  • GenotypeGVCFs produces bizarre mapping quality distribution
    • Daniel Nondorf
    • November 18, 2021 16:49
    0 votes 1 comment
  • GATK Non-model organism variant call SNP site all MQ same value
    • Bekah W
    • November 13, 2021 14:02
    0 votes 1 comment
  • 7 things I learned while reprocessing my WGS data on Terra: part 1
    • KT Pickard
    • June 14, 2021 21:49
    0 votes 1 comment
  • Picard CheckIlluminaDirectory - Issue with file/folder structure?
    • Jacob
    • June 14, 2021 19:52
    • Edited
    0 votes 1 comment
  • Why doesn't  haplotypecaller use PON?
    • sinc
    • June 04, 2021 05:11
    0 votes 1 comment
  • Somatic Structure Variation on exome-seq data
    • wiki97
    • October 22, 2020 09:26
    • Edited
    0 votes 1 comment
  • Sensitive Copy Ratio Pipeline compatibility with tool "mergeLevels"
    • Gannon Cottone
    • May 06, 2020 15:34
    0 votes 1 comment
  • Haplotype caller error "Exception in thread "main" java.lang.IncompatibleClassChangeError: Inconsistent constant pool data in classfile for class"
    • Anna Gatseva
    • March 22, 2023 11:00
    0 votes 0 comments
  • somatic CNV PoN
    • Sheryl
    • March 06, 2023 20:00
    • Edited
    0 votes 0 comments
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