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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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  • 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 9 comments
  • Checking ReadGroup name in BAM file with GATK instructions
    • Julianne Radford
    • February 16, 2021 19:04
    0 votes 1 comment
  • How to work with CNN variant caller
    • Danio Rerio
    • February 16, 2021 16:09
    0 votes 3 comments
  • Mitochondrial analysis - FilterMutectCalls autosomal-coverage is not an option
    • leory
    • February 16, 2021 13:42
    0 votes 1 comment
  • HaplotypeCaller and Read Group Errors
    • Julianne Radford
    • February 11, 2021 17:45
    0 votes 1 comment
  • DepthOfCoverage Error: Refseq file contains transcripts with zero coding length
    • ashgorden
    • February 04, 2021 08:15
    0 votes 2 comments
  • filterSamReads stdout format error
    • rcorbett
    • February 04, 2021 15:31
    • Edited
    0 votes 15 comments
  • Cromwell stuck at WaitingForReturnCode on Mac
    • Marc Crepeau
    • February 01, 2021 21:00
    0 votes 3 comments
  • Map reads with alternate contigs
    • Linda Do
    • January 30, 2021 22:22
    0 votes 1 comment
  • Reference Fasta vs Alt Reference Fasta
    • Linda Do
    • January 29, 2021 21:56
    0 votes 2 comments
  • Mutect2: NuMTs filtering on RNA-seq
    • Leore Nehemie Bensabath
    • January 29, 2021 15:57
    0 votes 1 comment
  • Realignment indels filtering 1000G
    • Hanna Söderström
    • January 26, 2021 14:06
    0 votes 1 comment
  • HaplotypeCaller -ERC GVCF -variant_index_type LINEAR
    • Matilde
    • January 22, 2021 18:22
    0 votes 1 comment
  • Why do I see difference in ploidy in GT field within same sample after GenotypeVCFs
    • Emila Mańko
    • January 21, 2021 17:54
    0 votes 3 comments
  • Comparison between ReadsPipelineSpark and MarkDuplicates
    • AMN
    • January 20, 2021 00:36
    • Edited
    0 votes 7 comments
  • Resource bundle hg38 hosts corrupted VCF
    • René Böttcher
    • January 18, 2021 11:42
    0 votes 1 comment
  • Resource bundle for GRCh37
    • Reda
    • January 17, 2021 17:38
    0 votes 1 comment
  • Funcotator missing AF
    • Haiying Kong
    • January 11, 2021 15:13
    0 votes 1 comment
  • MarkDuplicates
    • JAY SINGH
    • January 10, 2021 13:41
    0 votes 1 comment
  • ASEReadCounter java.lang.ArrayIndexOutOfBoundsException: 0
    • zhaol
    • January 08, 2021 07:38
    0 votes 3 comments
  • Any documents for 199 columns in Funcotator output?
    • Haiying Kong
    • January 07, 2021 10:03
    0 votes 2 comments
  • When the useful PGT and PID fields have been implemented in GATK tool for the first time
    • Sandrine lagarrigue
    • December 31, 2020 17:36
    0 votes 1 comment
  • Converting Reference Genomes from b37 to hg19
    • Abhi Agarwal
    • December 30, 2020 19:12
    0 votes 4 comments
  • How to merge approx 150 bam file using Picard
    • Shazia Kunvar
    • 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
  • Clarity on Variant Callers being "optimized for UMI-containing data"
    • Alijah O'Connor
    • December 18, 2020 00:49
    • Edited
    0 votes 1 comment
  • Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded when using gatk GetPileupSummaries
    • Will
    • December 17, 2020 16:02
    0 votes 1 comment
  • BQSR no output table found
    • Tamrin Chowdhury
    • December 17, 2020 07:20
    0 votes 3 comments
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