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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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Show answered All Planned Not planned Completed Answered No status Sort by newest post Newest post Recent activity Votes Comments
  • Refseq accession number and version number in Funcotator Answered
    • TMB
    • April 26, 2022 04:13
    0 votes 4 comments
  • CNNScoreVariants Issues with environment and Java version Answered
    • Kathrin B
    • April 13, 2022 15:07
    • Edited
    0 votes 6 comments
  • Fontconfig error in the newest gatk docker image Answered
    • SkyWarrior
    • April 10, 2022 09:02
    • Edited
    0 votes 1 comment
  • vulnerability issue for gatk-package-4.2.5.0-local.jar Answered
    • John Yu
    • March 09, 2022 14:27
    0 votes 4 comments
  • Local WDL Mitochondria Pipeline - Import failed Answered
    • Michael
    • March 08, 2022 09:25
    • Edited
    0 votes 1 comment
  • Error in GenomicsDBImport: Invalid deflate block found Answered
    • Lauren Hennelly
    • February 26, 2022 20:26
    1 vote 6 comments
  • GC overhead limit exceeded using Mutect2 only tumor version Answered
    • Shirliya Dadon
    • February 09, 2022 12:53
    • Edited
    0 votes 5 comments
  • GATK R plots with R v4.1.2 Answered
    • Franz Gassner
    • January 24, 2022 09:36
    0 votes 3 comments
  • Error in running GenomicsDBConfigException Answered
    • Shivangi Agarwal
    • December 20, 2021 14:51
    0 votes 12 comments
  • CollectRnaSeqMetrics GL000220 test not counting ribosomal reads Answered
    • rcorbett
    • December 06, 2021 18:45
    0 votes 5 comments
  • MarkduplicatesSpark failed Answered
    • lid.zigh
    • November 23, 2021 13:44
    0 votes 3 comments
  • Contamination calculation on single file don't detect contaminated samples Answered
    • Vladislav Maximov
    • October 14, 2021 15:03
    0 votes 7 comments
  • GenomincsDBImport Failed to create reader from file: An index is required, but none found., for input source: Answered
    • Morgan Sparks
    • October 12, 2021 11:46
    0 votes 6 comments
  • markduplicatesSpark .bam.parts output error (directory already exists) Answered
    • Morgan Sparks
    • September 30, 2021 16:31
    0 votes 3 comments
  • Funcotator gnomAD MAF columns Answered
    • TMB
    • August 23, 2021 02:04
    0 votes 2 comments
  • Can't explain the number of reads FilterSamReads outputs Answered
    • Aki Jarl Laruson
    • July 28, 2021 23:29
    0 votes 8 comments
  • GenomeSTRiP SVPreprocess failed Answered
    • Jenny Xu
    • July 27, 2021 02:46
    0 votes 3 comments
  • Hi Can you please point me to the chain file for human_g1k_v37_decoy to hg19 conversion Answered
    • smk_84
    • July 06, 2021 20:48
    • Edited
    0 votes 1 comment
  • Docker image for GATK3 version 3.7 Answered
    • Tatyana Zhuravleva
    • June 27, 2021 01:29
    0 votes 2 comments
  • Funcotator missing cDNA, Codon, and Protein Change for some chromosomes Answered
    • Robert Bremel
    • June 05, 2021 01:44
    0 votes 1 comment
  • Picard liftover Issue bostau8 to bostau6 Answered
    • Abrish
    • May 31, 2021 10:20
    0 votes 2 comments
  • DepthOfCoverage with -gene-list and readgroup as --partition-type options Answered
    • David Jaspez
    • May 06, 2021 14:58
    0 votes 7 comments
  • ApplyBQSR no positional argument is defined for this tool Answered
    • Jose Aragon
    • March 06, 2021 14:26
    0 votes 7 comments
  • Mitochondrial analysis - FilterMutectCalls autosomal-coverage is not an option Answered
    • leory
    • February 16, 2021 13:42
    0 votes 3 comments
  • Mutect2: NuMTs filtering on RNA-seq Answered
    • Leore Nehemie Bensabath
    • January 29, 2021 15:57
    0 votes 2 comments
  • Call-caching not functional running cromwell locally on GCP VM Answered
    • ibrahimkurt
    • December 08, 2020 16:40
    0 votes 9 comments
  • No results of CollectvariantCallingMetrics Answered
    • Yenan
    • November 30, 2020 07:13
    0 votes 30 comments
  • Truncated bam file after running ReplaceSamHeader(Picard) Answered
    • kostas alexiou
    • November 17, 2020 15:12
    0 votes 6 comments
  • Error in running SplitNCigarReads - htsjdk.samtools.util.RuntimeIOException Answered
    • KATHIE NGO
    • August 27, 2020 17:31
    • Edited
    0 votes 8 comments
  • --tmp-dir option user error Answered
    • Brynjar Sigurðsson
    • August 10, 2020 12:22
    0 votes 13 comments
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