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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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  • resource bundle b37
    • hirokomatsui
    • June 19, 2020 00:20
    0 votes 1 comment
  • MarkDuplicatesSparks not removing some duplicates?
    • Tom Morrison
    • June 18, 2020 14:55
    0 votes 15 comments
  • copyright issue
    • Özlem Okutman
    • June 16, 2020 13:17
    0 votes 2 comments
  • Genomestrip cannot find --ploidyMapFile
    • Swanthana Rekulapally
    • June 11, 2020 20:23
    0 votes 9 comments
  • IlluminaBasecallsToSam - barcode was not expected
    • Vincent Hahaut
    • June 10, 2020 19:04
    0 votes 1 comment
  • When will AnalyzeCovariates support R/4.0
    • Qi Yu
    • June 09, 2020 21:20
    0 votes 1 comment
  • Error when running FastaAlternateReferenceMaker
    • Fritz Forbang
    • June 09, 2020 10:27
    0 votes 1 comment
  • GenomicsDBImport does not recognize option --genomicsdb-update-workspace-path
    • Jose Luis Gualdron
    • June 08, 2020 08:08
    0 votes 2 comments
  • humanG1Kv37 to hg38 liftover issues
    • brian miller
    • June 06, 2020 00:44
    • Edited
    0 votes 3 comments
  • Error in running CollectGcBiasMetrics
    • SrivastavaS
    • June 05, 2020 17:30
    0 votes 1 comment
  • ReciprocalOverlapAnnotator error for Illumina data (both ERDS and CNVnator)
    • Ghausia Begum
    • June 04, 2020 04:22
    0 votes 5 comments
  • Mutect2: mitochondria mode weird
    • Roberto Sirica
    • June 03, 2020 14:46
    0 votes 2 comments
  • SelectVariants v4.1.6.0 doesn't select the variants as expected Answered
    • ABours
    • June 02, 2020 13:26
    0 votes 8 comments
  • VariantRecalibrator throwing VariantRecalibratorEngine - Evaluate datum returned a NaN warning then crashing with empty tranches file.
    • David Murphy
    • June 02, 2020 12:58
    • Edited
    0 votes 2 comments
  • something wrong with MarkDuplicatesSpark
    • charles_cai
    • June 02, 2020 10:09
    0 votes 1 comment
  • GenotypeGVCF Output Only 1 Locus
    • Himawari
    • June 01, 2020 11:47
    • Edited
    0 votes 1 comment
  • Can't open VCF File
    • Sanat Mishra
    • May 31, 2020 19:24
    0 votes 2 comments
  • newbie question: how to split a genome bam file by using picard
    • You Meng
    • May 30, 2020 10:00
    0 votes 8 comments
  • DepthofCoverage GATK4.1.7.0 -gene-list Answered
    • marta r
    • May 27, 2020 14:19
    0 votes 15 comments
  • CombineGVCF slowing down at certain region on chromosome 1
    • wd
    • May 26, 2020 18:38
    • Edited
    0 votes 3 comments
  • gatk4-mitochondria-pipeline Problems
    • Valentin Hildemann
    • May 26, 2020 16:18
    0 votes 1 comment
  • GenomeStrip prepare summary metadata by chromosome?
    • zzq
    • May 25, 2020 01:18
    0 votes 2 comments
  • Setting SPARK resources when using the gatk release version
    • Ury Alon
    • May 18, 2020 04:42
    • Edited
    0 votes 15 comments
  • No depth information in INFO column
    • Jay Singh
    • May 16, 2020 20:52
    0 votes 2 comments
  • Depthofcoverage interval summary file is empty
    • Sudha, Parvathi
    • May 14, 2020 15:07
    0 votes 1 comment
  • Recal file with malformed header
    • Erik Fasterius
    • May 14, 2020 09:43
    0 votes 9 comments
  • Read counts in vcf files do not reflect local realignments
    • jhb
    • May 13, 2020 15:22
    • Edited
    0 votes 2 comments
  • RemoveNearbyIndels: CRSP
    • Andrew Zhang
    • May 13, 2020 06:49
    0 votes 6 comments
  • HaplotypeCaller on multiple BAMs vs Joint-Call Cohort
    • lahl
    • May 12, 2020 20:21
    0 votes 3 comments
  • Output vcf file from HaplotypeCaller mostlly contain <NON_REF> alteration
    • Jay Singh
    • May 12, 2020 14:58
    0 votes 3 comments
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