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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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  • GATK for Rnor6 - Funcotator error
    • Ngoc Khoi Dang
    • August 03, 2022 16:30
    • Edited
    0 votes 0 comments
  • All intervals were filtered in Filterintervals
    • 侯旻
    • May 31, 2022 08:24
    0 votes 11 comments
  • Selectvariants for SNPs selection produces .vcf file without homozygous-REF calls
    • Amod Kumar
    • December 02, 2021 11:03
    0 votes 5 comments
  • GatherVcfs - File number limit?
    • rokkineste
    • November 22, 2021 12:14
    • Edited
    0 votes 3 comments
  • How do iquery VCF for specific variants by CHROM and POS
    • Alon Ziv
    • October 30, 2021 09:40
    0 votes 3 comments
  • No downsampling with max-reads-per-alignment-start
    • Liang Ye
    • October 28, 2021 01:37
    • Edited
    0 votes 3 comments
  • GenomicsDBimport and CombineGVCF does not show variants at ~500 Mbp onwards, although gvcf files from HapolypeCaller report variants
    • Hanin
    • September 27, 2021 07:22
    • Edited
    0 votes 5 comments
  • is it ok to apply BQSR and HaplotypeCaller to autosome noncoding region by -L by chromoosme?
    • Shanshan
    • September 09, 2021 02:44
    0 votes 2 comments
  • Preform variant calling on 50 bp SE rna-seq data
    • Alon Ziv
    • September 03, 2021 05:35
    0 votes 4 comments
  • GenotypeGVCF too many genotypes
    • Victoria Buswell
    • June 04, 2021 10:40
    0 votes 1 comment
  • A USER ERROR has occurred: Badly formed genome unclippedLoc: Query interval "-e xxxx" is not valid for this input when use GenomicsDBImport.
    • Troy
    • April 28, 2021 02:16
    0 votes 1 comment
  • Unexpected SOR value changes
    • Luca Marcolungo
    • April 14, 2021 20:04
    0 votes 1 comment
  • Haplotypecaller produce unfinished vcf but no idx (no error)
    • Lin Cheng
    • March 30, 2021 09:24
    0 votes 13 comments
  • CallableLoci on Triticum species
    • Barbara Iadarola
    • March 17, 2021 11:48
    0 votes 1 comment
  • 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
  • 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
  • Error Running IndexFeatureFile on Ensembl Mouse GTF file
    • T. Li
    • January 25, 2021 04:38
    • Edited
    0 votes 1 comment
  • 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
  • the reads covering the special location between before HaplotypeCaller and after HaplotypeCaller
    • yunxin.f
    • December 23, 2020 08:51
    0 votes 1 comment
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