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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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New User Advice

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Show all All Planned Not planned Completed Answered No status Sort by newest post Newest post Recent activity Votes Comments
  • WARN InbreedingCoeff - InbreedingCoeff will not be calculated at position chr1:40 and possibly subsequent; at least 10 samples must have called genotypes Answered
    • Dina Tzur
    • March 13, 2022 16:46
    0 votes 3 comments
  • GATK MarkDuplicatesSpark output error Answered
    • Bilge Tabak
    • March 11, 2022 17:39
    0 votes 3 comments
  • How to provide custom exon-intron annotation source in Funcotator
    • Elisabetta Manduchi
    • February 18, 2022 13:48
    0 votes 4 comments
  • AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '<optimized capture of last three': 'separated fields as numeric values>' did not match read name '2hpf_wt_total_SRR870747.42096'. Answered
    • Dina Tzur
    • February 06, 2022 12:01
    0 votes 11 comments
  • What should I do with vcf file now Answered
    • mina ming
    • February 03, 2022 13:20
    • Edited
    0 votes 1 comment
  • ApplyBQSR for somatic mutation detection in HLA regions Answered
    • Elisabetta Manduchi
    • February 01, 2022 17:07
    0 votes 7 comments
  • Where is my GATK4 ? Answered
    • MianQi
    • December 20, 2021 10:15
    • Edited
    0 votes 1 comment
  • Pileup output of GATK4 vs. GATK3 Answered
    • Ran Wei
    • December 02, 2021 01:37
    0 votes 1 comment
  • bash: gatk: command not found Answered
    • Jeremy Sutherland
    • December 01, 2021 19:20
    0 votes 2 comments
  • GATK GenomicsDBImport intervals Answered
    • Bekah W
    • November 26, 2021 14:23
    0 votes 19 comments
  • rename sample in GVCF file Answered
    • Bekah W
    • November 23, 2021 22:08
    0 votes 3 comments
  • GenotypeGVCFs produces bizarre mapping quality distribution
    • Daniel Nondorf
    • November 18, 2021 16:49
    0 votes 1 comment
  • GATK Non-model organism variant call SNP site all MQ same value
    • Bekah W
    • November 13, 2021 14:02
    0 votes 1 comment
  • MarkDuplicates analysis of large wheat chromosomes Answered
    • John Baison
    • November 11, 2021 11:54
    0 votes 2 comments
  • ApplyBQSR doesn't recognise my arguments? Answered
    • Ali Hudson
    • November 10, 2021 15:55
    • Edited
    0 votes 3 comments
  • Exclude non variant sites Answered
    • Victoria Buswell
    • October 27, 2021 15:26
    0 votes 1 comment
  • Using GATK as a genotyper to genotype existing variants Answered
    • Ivar Grytten
    • October 12, 2021 13:53
    0 votes 6 comments
  • GATK4.0.3.0 - CombineGVCFs - Unexpected base in allele bases
    • HT
    • October 01, 2021 05:28
    0 votes 4 comments
  • Mutect2 somatic mutation calling for plant
    • Lina Herliana
    • September 15, 2021 01:42
    0 votes 2 comments
  • Help with running GATK RNAseq workflow with docker backend and multiple cpus?
    • ThyagoLC
    • September 02, 2021 15:38
    • Edited
    0 votes 3 comments
  • Empty intersection error when applying intervals Answered
    • Ran Wei
    • August 31, 2021 22:33
    0 votes 3 comments
  • Script for using same GATK tool(s) on multiple sample files Answered
    • Youssef Tawfik
    • August 01, 2021 16:32
    0 votes 1 comment
  • Creating dictionary for fasta reeference file Answered
    • Priyadarshini Thirunavukkarasu
    • July 30, 2021 09:24
    • Edited
    0 votes 1 comment
  • GQ in jointly genotyped samples Answered
    • stelmaria
    • July 29, 2021 21:11
    0 votes 1 comment
  • Combining mplileup and haplotypeCaller calls Answered
    • Charlotte Her
    • July 22, 2021 17:03
    0 votes 2 comments
  • Help with WDL workflow for mutec2? Answered
    • Alex Lee
    • July 14, 2021 17:01
    0 votes 5 comments
  • looking for panel of normals and allele frequency for hg19 genome build Answered
    • elhadi iich
    • June 30, 2021 09:47
    0 votes 1 comment
  • picard CollectAlignmentSummaryMetrics required arguments format Answered
    • Serge
    • June 28, 2021 19:20
    0 votes 1 comment
  • gatk legacy bundles (where to get Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz) Answered
    • Nick Kinney
    • June 24, 2021 16:08
    0 votes 3 comments
  • ValiidateSamFile Error: Mate not found Answered
    • Stephen Johnson
    • June 17, 2021 14:39
    0 votes 13 comments
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