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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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Somatic

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Show all All Planned Not planned Completed Answered No status Sort by newest post Newest post Recent activity Votes Comments
  • Do read group names have effect on marking duplicates using GATK?
    • halo
    • January 28, 2021 04:29
    0 votes 1 comment
  • GATK Funcotator missing DP and AF information from vcf file
    • Haiying Kong
    • January 27, 2021 12:18
    0 votes 3 comments
  • GATK Funcotator Variant_Classification
    • Haiying Kong
    • January 27, 2021 11:37
    0 votes 1 comment
  • No headers found in VCF
    • Qing Zhang
    • January 26, 2021 17:42
    0 votes 2 comments
  • Some of variants detected by the Mutect2 are contradictory
    • rime
    • January 26, 2021 13:13
    0 votes 3 comments
  • af-only-gnomad.hg38.vcf.gz details
    • lmose
    • January 25, 2021 18:48
    0 votes 8 comments
  • Funcotator to annotate VCF files with structural variants
    • Lucia C
    • January 21, 2021 20:16
    0 votes 2 comments
  • Broad hg19 TWIST interval list Answered
    • Tejas Jammihal
    • January 20, 2021 17:14
    1 vote 4 comments
  • CreateSomaticPanelOfNormals: can a panel of normals be created from more than one GenomicsDB workspace?
    • ISmolicz
    • January 20, 2021 13:18
    • Edited
    0 votes 2 comments
  • GetPileupSummaries get only header and no output
    • xiaotian shen
    • January 19, 2021 08:37
    0 votes 1 comment
  • Sample does not have a non-negative sample median when running DenoiseReadCounts to test the example data Tutorial11682
    • Yuanyuan Wu
    • January 13, 2021 17:32
    0 votes 7 comments
  • No Output from GenomicsDBImport
    • vivekruhela
    • January 12, 2021 19:16
    0 votes 2 comments
  • is it possible to use a gcs bucket directory as tmp directory?
    • joy bordini
    • January 07, 2021 19:08
    0 votes 3 comments
  • [Repost] Wrong annotation with Funcotator 1.7 Answered
    • A. Brink
    • January 11, 2021 13:14
    • Edited
    0 votes 10 comments
  • The missing value in Mutect2 vcf
    • Hsu Pei-Chun
    • January 06, 2021 02:33
    0 votes 2 comments
  • Empty final PON vcf file from 7 samples Answered
    • Yun Yu
    • January 04, 2021 08:42
    0 votes 18 comments
  • The missing value in Mutect2 vcf
    • Hsu Pei-Chun
    • December 31, 2020 05:16
    0 votes 2 comments
  • How mutect2 panel of normal works? Answered
    • Joe
    • December 22, 2020 08:44
    0 votes 8 comments
  • "no suitable codecs found" by using CreateSomaticPanelOfNormals
    • Hsu Pei-Chun
    • December 21, 2020 08:40
    0 votes 1 comment
  • Mutect2 PON VCF
    • avrajit
    • December 19, 2020 03:15
    0 votes 3 comments
  • Bamout haplotypes are much worse than bamout tumor reads would suggest
    • Alijah O'Connor
    • December 18, 2020 17:43
    0 votes 1 comment
  • Wrong annotation with Funcotator 1.7
    • A. Brink
    • December 18, 2020 12:46
    0 votes 3 comments
  • Empty final PON vcf file from 7 samples
    • Yun Yu
    • December 18, 2020 08:44
    0 votes 2 comments
  • How to use UpdateVCFSequenceDictionary if I don't have any input VCF files?
    • rahelp
    • December 14, 2020 11:21
    0 votes 9 comments
  • GATK4 MUTECT2 missed some variants in the raw vcf
    • LUO XI
    • December 14, 2020 10:17
    0 votes 2 comments
  • How do I add allele depth to Mutect2 output?
    • Ashi
    • December 12, 2020 22:23
    0 votes 2 comments
  • Mutect2 strand_bias problem
    • hansonl
    • December 11, 2020 02:29
    0 votes 2 comments
  • Sequence dictionary and index contain different numbers of contigs
    • rahelp
    • December 09, 2020 07:19
    0 votes 4 comments
  • Is BQSR accurate on Novaseq 6000?
    • Tom van den Bosch
    • December 08, 2020 09:27
    0 votes 3 comments
  • Cromwell: can't find file ID
    • Stephanie Hoyt
    • December 07, 2020 19:58
    0 votes 1 comment
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