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Genome Analysis Toolkit

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
  • FilterMutectCalls didn't filtered any variants for my vcf file Answered
    • Xiya Song
    • February 28, 2021 11:02
    0 votes 3 comments
  • Mutect2 - Joint calling Answered
    • Yen-Ping Yeh
    • February 23, 2021 08:44
    0 votes 8 comments
  • HaplotypeCaller VCF for PON
    • Steven Bentley
    • February 22, 2021 23:05
    0 votes 3 comments
  • 1 year-old bug in libgkl that has not been fixed affecting FilterAlignmentArtifacts and HaplotypeCaller
    • GE
    • February 18, 2021 23:16
    0 votes 3 comments
  • Bug: Badly formed genome unclippedLoc
    • GE
    • February 16, 2021 22:43
    0 votes 12 comments
  • FilterMutectCalls --unique-alt-read-count argument
    • Greg Goralogia
    • February 16, 2021 20:48
    0 votes 10 comments
  • Panel of normals for Mutect2 GRCh37
    • nhaus
    • February 14, 2021 17:51
    • Edited
    0 votes 2 comments
  • mutect2 error: "Unknown file is malformed: Could not read sequence dictionary from given fasta file refereces.dict" Answered
    • zdr j
    • February 12, 2021 09:55
    • Edited
    0 votes 6 comments
  • Error initializing feature reader for path somatic-hg38_1000g_pon.hg38.vcf.gz Answered
    • Tim Bishop
    • February 11, 2021 23:25
    0 votes 8 comments
  • SNP analysis returning way too many variants
    • dodausp
    • February 11, 2021 11:20
    • Edited
    0 votes 2 comments
  • Funcotator does not work on hg19
    • Yosef Maruvka
    • February 09, 2021 14:06
    0 votes 1 comment
  • Error was: Sequence dictionary and index contain different numbers of contigs
    • Adam Session
    • February 08, 2021 23:18
    0 votes 7 comments
  • Mutect2 for ATAC-seq?
    • Елизавета Александровна Миноцкая
    • February 08, 2021 13:35
    0 votes 1 comment
  • Question GetPileupSummaries, columns all 0
    • Brian Wiley
    • February 03, 2021 05:53
    • Edited
    0 votes 6 comments
  • QUAL values not present in Mutect2 VCF
    • Alfonso Lam
    • February 01, 2021 15:34
    0 votes 2 comments
  • GetPileupSummaries error
    • Aqshin Balayev
    • January 31, 2021 23:00
    0 votes 4 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 6 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
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