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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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Non-Human

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Show all All Planned Not planned Completed Answered No status Sort by comments Newest post Recent activity Votes Comments
  • GenotypeGVCFs stalls while using --all-sites Answered
    • Rachael Bay
    • September 15, 2020 22:13
    0 votes 37 comments
  • gatk HaplotypeCaller gives me an empty vcf Answered
    • Marie Saitou
    • January 23, 2021 10:12
    0 votes 18 comments
  • GenomicsDBimport not importing all the batches
    • Vinod Kumar
    • January 20, 2021 14:56
    • Edited
    0 votes 18 comments
  • GenomicsDBImport very slow on genome with many contigs Answered
    • Marley Yeong
    • April 02, 2020 15:22
    1 vote 17 comments
  • Speeding up GenotypeGVCFS? GATK4 Answered
    • Cecilia Kardum Hjort
    • May 13, 2020 09:16
    0 votes 16 comments
  • emit-ref-confidence error Answered
    • Florence Morel
    • December 28, 2020 17:38
    0 votes 15 comments
  • Haplotypecaller produce unfinished vcf but no idx (no error)
    • Lin Cheng
    • March 30, 2021 09:24
    0 votes 13 comments
  • Error Creatting Dictionary for genome Answered
    • Abrish
    • December 15, 2020 12:19
    • Edited
    0 votes 12 comments
  • All intervals were filtered in Filterintervals
    • 侯旻
    • May 31, 2022 08:24
    0 votes 11 comments
  • Issues while running GenotypeGVCFs Answered
    • sanjeevksh
    • June 25, 2021 04:16
    • Edited
    0 votes 11 comments
  • Provider "genedb" not found when using SelectVariants & GenomicsDBImport
    • Lucas Carey
    • March 12, 2020 02:00
    0 votes 11 comments
  • StrandBiasBySample SB in vcf Answered
    • 羅Pichu
    • February 28, 2021 22:47
    0 votes 10 comments
  • Getting an error with genomicsdbimport
    • Vinod Kumar
    • November 09, 2020 16:35
    • Edited
    0 votes 9 comments
  • Unphased homozyous sites between phased heterozygous sites
    • OzAy
    • January 14, 2020 19:39
    • Edited
    0 votes 9 comments
  • java.lang.IllegalStateException in GenotypeGVCFs after GenomicsDBImport, GATK 4.2.6.1 Answered
    • Zane Swaydan
    • June 30, 2022 11:38
    • Edited
    0 votes 8 comments
  • ApplyBQSR to unmapped reads for non-model organism does not work with '-L unmapped' flag
    • cali
    • September 02, 2020 23:17
    0 votes 8 comments
  • A USER ERROR has occurred: Badly formed genome unclippedLoc: Parameters to GenomeLocParser are incorrect:The stop position 0 is less than start 1 in contig contig004333 Answered
    • New_gatk_user
    • August 04, 2020 11:43
    • Edited
    0 votes 8 comments
  • GenotypeGvcfs has formatting issues in both v4.1.6.0 as v4.1.7.0
    • ABours
    • May 29, 2020 18:23
    0 votes 8 comments
  • StrandBiasBySample error Haplotypecaller
    • gubrins
    • May 11, 2020 14:39
    0 votes 8 comments
  • bqsr output issue
    • John Denton
    • April 21, 2020 16:01
    0 votes 8 comments
  • HaplotypeCaller local Assembly
    • Etergemina
    • April 21, 2020 09:37
    • Edited
    0 votes 8 comments
  • Empty vcf after GenotypeVCFs when combining already genotyped samples
    • leze
    • April 08, 2020 22:40
    0 votes 8 comments
  • Error running HaplotypeCaller?
    • vctrymao
    • January 08, 2020 15:42
    0 votes 8 comments
  • GATK GenotypeGVCFs stuck on starting traversal Answered
    • Mary Happ
    • November 11, 2021 19:38
    • Edited
    0 votes 7 comments
  • VariantFiltration Answered
    • ThierryGrange
    • February 25, 2021 19:37
    0 votes 7 comments
  • Keras error in CNNScoreVariants
    • jodybk
    • February 11, 2021 15:20
    0 votes 7 comments
  • VQSR: how is insufficient variance inferred for annotations? Answered
    • timh
    • January 26, 2021 10:57
    0 votes 7 comments
  • FixMateInformation does not solve ERROR:MATE_NOT_FOUND
    • Simon Hellemans
    • November 14, 2020 07:09
    • Edited
    1 vote 7 comments
  • Missing MQ scores in gvcf
    • Heather Tuttle
    • October 26, 2020 22:22
    0 votes 7 comments
  • HaplotypeCaller for haploid genome
    • Pummi Singh
    • September 06, 2020 23:30
    0 votes 7 comments
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