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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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  • 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
  • GATK for Rnor6 - Funcotator error
    • Ngoc Khoi Dang
    • August 03, 2022 16:30
    • Edited
    0 votes 0 comments
  • Speeding up GenotypeGVCFS? GATK4 Answered
    • Cecilia Kardum Hjort
    • May 13, 2020 09:16
    0 votes 16 comments
  • All intervals were filtered in Filterintervals
    • 侯旻
    • May 31, 2022 08:24
    0 votes 11 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
  • How do I call germline variants with multiple samples -non human? Answered
    • Jody Hey
    • November 20, 2020 16:15
    0 votes 5 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
  • GenotypeGVCFs stalls while using --all-sites Answered
    • Rachael Bay
    • September 15, 2020 22:13
    0 votes 37 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
  • StrandBiasBySample error Haplotypecaller
    • gubrins
    • May 11, 2020 14:39
    0 votes 8 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
  • GenomicsDBimport not importing all the batches
    • Vinod Kumar
    • January 20, 2021 14:56
    • Edited
    0 votes 18 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
  • VariantFiltration undefined variable Answered
    • wbsimey
    • July 05, 2020 16:35
    0 votes 5 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
  • ArtificialHaplotypeRG makes variant heterozygous Answered
    • Wiebe Kooistra
    • September 29, 2021 14:34
    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
  • GenomicsDBImport very slow on genome with many contigs Answered
    • Marley Yeong
    • April 02, 2020 15:22
    1 vote 17 comments
  • GATK 4.1.7.0 error java.lang.IllegalArgumentException: malformed input off : 17635906, length : 1
    • Sibelle Vilaça
    • May 23, 2020 12:51
    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
  • Error Creatting Dictionary for genome Answered
    • Abrish
    • December 15, 2020 12:19
    • Edited
    0 votes 12 comments
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