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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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New User Advice

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Show answered All Planned Not planned Completed Answered No status Sort by comments Newest post Recent activity Votes Comments
  • Error, ShouldNeverReachHereException, FuncotationMap in FilterFuncotations Answered
    • Joyce Anon
    • April 25, 2022 06:30
    0 votes 20 comments
  • GATK GenomicsDBImport intervals Answered
    • Bekah W
    • November 26, 2021 14:23
    0 votes 19 comments
  • ReadsPipelineSparkMulticore.wdl, Unrecognized runtime attribute keys: discs, cpu Answered
    • Andrew Erzunov
    • April 19, 2022 20:40
    • Edited
    0 votes 13 comments
  • ValiidateSamFile Error: Mate not found Answered
    • Stephen Johnson
    • June 17, 2021 14:39
    0 votes 13 comments
  • AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '<optimized capture of last three': 'separated fields as numeric values>' did not match read name '2hpf_wt_total_SRR870747.42096'. Answered
    • Dina Tzur
    • February 06, 2022 12:01
    0 votes 11 comments
  • ApplyBQSR for somatic mutation detection in HLA regions Answered
    • Elisabetta Manduchi
    • February 01, 2022 17:07
    0 votes 7 comments
  • Unclear why Picard ValidateSamFile is producing an error Answered
    • LOIC TALIGNANI
    • November 15, 2022 09:51
    0 votes 6 comments
  • Using GATK as a genotyper to genotype existing variants Answered
    • Ivar Grytten
    • October 12, 2021 13:53
    0 votes 6 comments
  • A USER ERROR has occurred: Contig chr1_KI270762v1_alt not present in reads sequence dictionary Answered
    • Maha Tageldein
    • June 06, 2022 05:03
    0 votes 5 comments
  • Help with WDL workflow for mutec2? Answered
    • Alex Lee
    • July 14, 2021 17:01
    0 votes 5 comments
  • Find rate of homozygosity Answered
    • Joyce Anon
    • July 28, 2022 05:12
    0 votes 4 comments
  • Suggestions to find pathogenic variant Answered
    • Joyce Anon
    • May 03, 2022 20:57
    0 votes 4 comments
  • CollectSamErrorMetrics error Answered
    • Joe Georgeson
    • October 10, 2022 17:41
    0 votes 3 comments
  • VariantFiltration issue Answered
    • Theresa Saunders
    • September 09, 2022 20:41
    0 votes 3 comments
  • Package ‘gsalib’ was removed from the CRAN repository. Answered
    • igor
    • July 13, 2022 15:56
    0 votes 3 comments
  • Proper way to prepare .bam for MarkDuplicatesSpark Answered
    • samuel
    • July 06, 2022 06:46
    1 vote 3 comments
  • GenomicsDBImport - why "intervals" is required?? Answered
    • Jianying Li
    • May 25, 2022 00:39
    0 votes 3 comments
  • Gatk4 rnaseq germline snps indels json file Answered
    • Alan Foley
    • May 19, 2022 10:29
    • Edited
    0 votes 3 comments
  • Variant Quality Score Recalibration Answered
    • Jakub S
    • May 09, 2022 15:27
    0 votes 3 comments
  • How to use WGA Data in picard Answered
    • Marcus Varni
    • May 03, 2022 23:13
    0 votes 3 comments
  • GATK working, but -ERC command not found Answered
    • Ann W
    • April 12, 2022 15:06
    0 votes 3 comments
  • WARN InbreedingCoeff - InbreedingCoeff will not be calculated at position chr1:40 and possibly subsequent; at least 10 samples must have called genotypes Answered
    • Dina Tzur
    • March 13, 2022 16:46
    0 votes 3 comments
  • GATK MarkDuplicatesSpark output error Answered
    • Bilge Tabak
    • March 11, 2022 17:39
    0 votes 3 comments
  • rename sample in GVCF file Answered
    • Bekah W
    • November 23, 2021 22:08
    0 votes 3 comments
  • ApplyBQSR doesn't recognise my arguments? Answered
    • Ali Hudson
    • November 10, 2021 15:55
    • Edited
    0 votes 3 comments
  • Empty intersection error when applying intervals Answered
    • Ran Wei
    • August 31, 2021 22:33
    0 votes 3 comments
  • gatk legacy bundles (where to get Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz) Answered
    • Nick Kinney
    • June 24, 2021 16:08
    0 votes 3 comments
  • Mutect2 with and without UMI information Answered
    • Davy Deng
    • June 16, 2021 15:34
    0 votes 3 comments
  • Invalid or corrupt jar file Answered
    • Shaun Clare
    • April 28, 2021 23:43
    0 votes 3 comments
  • Problems with FastQtoSAM Answered
    • Siddharth Prakash
    • April 09, 2021 14:00
    0 votes 3 comments
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