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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-microbialmode.jar
    • Jian Wang
    • March 23, 2023 21:33
    0 votes 0 comments
  • known-sites for Felis_catus_9.0 (GCA_000181335.4) Answered
    • Vladimir Makarov
    • March 15, 2023 20:16
    0 votes 4 comments
  • How to remove strand bias from a virus-derived signal-end NGS dataset
    • Fadi Alnaji
    • March 02, 2023 08:26
    0 votes 4 comments
  • HaplotypeCaller not calling variants in the beginning of an alignment (except when --alleles is specified)
    • Bert Bogaerts
    • February 03, 2023 16:09
    0 votes 1 comment
  • Tribble never saw the required #CHROM header, but it is there for the program GenomicsDBImport
    • Zubayr Ahmad
    • January 23, 2023 17:08
    0 votes 2 comments
  • GATK HaplotypeCaller for non-model organism: gVCF output
    • Katie
    • January 12, 2023 18:17
    0 votes 0 comments
  • Somatic Variant Calling for a non-model species not finding any variants
    • Isabella Livingston
    • January 09, 2023 16:58
    0 votes 0 comments
  • GenotypeGVCF error
    • Akshaya Vasudevan
    • December 01, 2022 17:39
    • Edited
    0 votes 0 comments
  • The expected variants were not detected for pig RNA-seq by GATK
    • Wen-ye Yao
    • October 24, 2022 14:12
    • Edited
    1 vote 8 comments
  • GatherVcfs to concatenate GVCFs
    • sanjeevksh
    • October 22, 2022 00:38
    0 votes 3 comments
  • GenotypeGvcf tetraploids as diploids Answered
    • julien leuenberger
    • August 12, 2022 09:26
    0 votes 4 comments
  • GATK for Rnor6 - Funcotator error Answered
    • Ngoc Khoi Dang
    • August 03, 2022 16:30
    • Edited
    0 votes 1 comment
  • 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
  • All intervals were filtered in Filterintervals
    • 侯旻
    • May 31, 2022 08:24
    0 votes 11 comments
  • FindBreakpointEvidenceSpark sudden shutdown Answered
    • Domniki Manousi
    • March 07, 2022 12:01
    0 votes 4 comments
  • emit-ref-confidence error Answered
    • Camila Martínez Avila
    • February 08, 2022 00:44
    0 votes 3 comments
  • gatk4-4.2.4.0-0 Fixmate Error Answered
    • Abrish
    • January 26, 2022 10:25
    • Edited
    0 votes 2 comments
  • GATK HaplotypeCaller disable filter -DF with the error in positional argument value Answered
    • Frans Dany
    • January 14, 2022 03:00
    0 votes 1 comment
  • VariantEval does not work or something wrong with my ref genome and dbsnps? Answered
    • Anh Mai
    • January 04, 2022 10:45
    0 votes 5 comments
  • ValidateSamFile Error Answered
    • Abrish
    • January 04, 2022 14:11
    • Edited
    0 votes 1 comment
  • Query regarding CombineGVCFs Answered
    • Abrish
    • December 20, 2021 17:54
    0 votes 4 comments
  • Inconsistent variant call in some pool-seq samples Answered
    • Lorena
    • December 10, 2021 15:53
    0 votes 3 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
  • GATK GenotypeGVCFs stuck on starting traversal Answered
    • Mary Happ
    • November 11, 2021 19:38
    • Edited
    0 votes 7 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
  • ArtificialHaplotypeRG makes variant heterozygous Answered
    • Wiebe Kooistra
    • September 29, 2021 14:34
    0 votes 5 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 7 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
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