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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 newest post Newest post Recent activity Votes Comments
  • GATK HaplotypeCaller OS Error - non-existent file or directory
    • Daniela Zarate
    • March 11, 2021 17:55
    • Edited
    0 votes 3 comments
  • Where are the sample-level annotations?
    • Marc Crepeau
    • March 05, 2021 02:00
    0 votes 1 comment
  • SAME READS has DIFFERENT VARIANTs
    • Lei Xia
    • March 04, 2021 02:07
    0 votes 1 comment
  • StrandBiasBySample SB in vcf Answered
    • 羅Pichu
    • February 28, 2021 22:47
    0 votes 10 comments
  • VariantFiltration Answered
    • ThierryGrange
    • February 25, 2021 19:37
    0 votes 7 comments
  • Issues with running GatherVcfs and SortVcfs (support+id105159@gatk.zendesk.com)
    • sanjeevksh
    • February 19, 2021 17:36
    0 votes 1 comment
  • Error: ValidateSamFile Value was put into PairInfoMap more than once.
    • Stephen Johnson
    • February 12, 2021 21:08
    0 votes 3 comments
  • output stuck in GenotypeGVCFs
    • tengMX
    • February 12, 2021 15:32
    0 votes 1 comment
  • Keras error in CNNScoreVariants
    • jodybk
    • February 11, 2021 15:20
    0 votes 7 comments
  • MarkDuplicatesSpark running, but not sorting/creating deduped bam files
    • Vai Pathak
    • February 09, 2021 20:58
    0 votes 3 comments
  • "No positional argument is defined" Error in HaplotypeCaller
    • Julianne Radford
    • February 06, 2021 21:07
    0 votes 5 comments
  • About Bam file input problem in HaplotypCaller
    • 酒香彈箏
    • February 03, 2021 08:42
    • Edited
    0 votes 6 comments
  • CombineGVCFs splitting MNPs into individual positions
    • Gabriel Margarido
    • January 31, 2021 01:01
    0 votes 6 comments
  • VQSR: how is insufficient variance inferred for annotations? Answered
    • timh
    • January 26, 2021 10:57
    0 votes 7 comments
  • Error Running IndexFeatureFile on Ensembl Mouse GTF file
    • T. Li
    • January 25, 2021 04:38
    • Edited
    0 votes 1 comment
  • 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
  • haplotypecallerspark wants DS_Store
    • John Denton
    • January 14, 2021 14:53
    0 votes 6 comments
  • Missing samples from the output vcf file produced with GenotypeGVCFs
    • Patrícia H. Brito
    • January 08, 2021 11:41
    0 votes 5 comments
  • emit-ref-confidence error Answered
    • Florence Morel
    • December 28, 2020 17:38
    0 votes 15 comments
  • the reads covering the special location between before HaplotypeCaller and after HaplotypeCaller
    • yunxin.f
    • December 23, 2020 08:51
    0 votes 1 comment
  • Genome STRiP - The output file of SVDiscovery is empty
    • latte kim
    • December 22, 2020 06:51
    0 votes 4 comments
  • REAL Variant not called by HaplotypeCaller Answered
    • HASSAN BADRANE
    • December 15, 2020 23:45
    1 vote 4 comments
  • Error Creatting Dictionary for genome Answered
    • Abrish
    • December 15, 2020 12:19
    • Edited
    0 votes 12 comments
  • MarkDuplicatesSpark not working on Putty
    • Robinn Teoh
    • December 15, 2020 03:39
    • Edited
    0 votes 1 comment
  • Weird log of genotypeGVCF
    • Vinod Kumar
    • December 11, 2020 15:46
    0 votes 1 comment
  • Why is GenotypeGVCF taking a long time for a smaller genome?
    • Vinod Kumar
    • December 07, 2020 14:05
    • Edited
    0 votes 4 comments
  • Exclude-intervals error with PathSeq
    • Wir963
    • November 25, 2020 17:13
    0 votes 1 comment
  • How do I call germline variants with multiple samples -non human? Answered
    • Jody Hey
    • November 20, 2020 16:15
    0 votes 5 comments
  • FixMateInformation does not solve ERROR:MATE_NOT_FOUND
    • Simon Hellemans
    • November 14, 2020 07:09
    • Edited
    1 vote 7 comments
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