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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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Show answered All Planned Not planned Completed Answered No status Sort by comments Newest post Recent activity Votes Comments
  • No results of CollectvariantCallingMetrics Answered
    • Yenan
    • November 30, 2020 07:13
    0 votes 30 comments
  • Panel of Normals Documentation Answered
    • Ryan Gimple
    • April 16, 2020 17:48
    1 vote 16 comments
  • DepthofCoverage GATK4.1.7.0 -gene-list Answered
    • marta r
    • May 27, 2020 14:19
    0 votes 15 comments
  • --tmp-dir option user error Answered
    • Brynjar Sigurðsson
    • August 10, 2020 12:22
    0 votes 13 comments
  • CNNScoreVariants carshes with java.lang.NullPointerException Answered
    • riederd
    • January 17, 2020 15:29
    1 vote 13 comments
  • Error in running GenomicsDBConfigException Answered
    • Shivangi Agarwal
    • December 20, 2021 14:51
    0 votes 12 comments
  • GenomeStrip SVPreprocess works with for a chromosome region; but fail for whole genome Answered
    • APato
    • February 03, 2020 21:28
    0 votes 10 comments
  • Call-caching not functional running cromwell locally on GCP VM Answered
    • ibrahimkurt
    • December 08, 2020 16:40
    0 votes 9 comments
  • GenomicsDBImport: Attempting to genotype more than 50 alleles Answered
    • Nils Homer
    • August 06, 2020 00:13
    1 vote 9 comments
  • Can't explain the number of reads FilterSamReads outputs Answered
    • Aki Jarl Laruson
    • July 28, 2021 23:29
    0 votes 8 comments
  • Error in running SplitNCigarReads - htsjdk.samtools.util.RuntimeIOException Answered
    • KATHIE NGO
    • August 27, 2020 17:31
    • Edited
    0 votes 8 comments
  • SelectVariants v4.1.6.0 doesn't select the variants as expected Answered
    • ABours
    • June 02, 2020 13:26
    0 votes 8 comments
  • Contamination calculation on single file don't detect contaminated samples Answered
    • Vladislav Maximov
    • October 14, 2021 15:03
    0 votes 7 comments
  • DepthOfCoverage with -gene-list and readgroup as --partition-type options Answered
    • David Jaspez
    • May 06, 2021 14:58
    0 votes 7 comments
  • ApplyBQSR no positional argument is defined for this tool Answered
    • Jose Aragon
    • March 06, 2021 14:26
    0 votes 7 comments
  • Accessing the resource bundle. Answered
    • nagam surya
    • June 28, 2022 18:35
    0 votes 6 comments
  • CNNScoreVariants Issues with environment and Java version Answered
    • Kathrin B
    • April 13, 2022 15:07
    • Edited
    0 votes 6 comments
  • Error in GenomicsDBImport: Invalid deflate block found Answered
    • Lauren Hennelly
    • February 26, 2022 20:26
    1 vote 6 comments
  • GenomincsDBImport Failed to create reader from file: An index is required, but none found., for input source: Answered
    • Morgan Sparks
    • October 12, 2021 11:46
    0 votes 6 comments
  • Truncated bam file after running ReplaceSamHeader(Picard) Answered
    • kostas alexiou
    • November 17, 2020 15:12
    0 votes 6 comments
  • FindBadGenomicKmersSpark running indefinitely Answered
    • Cher Wei Yuan
    • August 02, 2022 02:25
    0 votes 5 comments
  • Hard filters on VariantFiltration following HaplotypeCaller; Filter contains an illegal character Answered
    • Graeme Thorn
    • May 27, 2022 21:05
    • Edited
    0 votes 5 comments
  • GC overhead limit exceeded using Mutect2 only tumor version Answered
    • Shirliya Dadon
    • February 09, 2022 12:53
    • Edited
    0 votes 5 comments
  • CollectRnaSeqMetrics GL000220 test not counting ribosomal reads Answered
    • rcorbett
    • December 06, 2021 18:45
    0 votes 5 comments
  • MarkduplicatesSpark failed Answered
    • lid.zigh
    • November 23, 2021 13:44
    0 votes 5 comments
  • ShiftFasta creates empty intervals file Answered
    • Ram
    • October 21, 2022 07:56
    • Edited
    0 votes 4 comments
  • How can I build the GATK jar so that the intel native libraries are available? Answered
    • Mark Schreiber
    • September 22, 2022 16:49
    0 votes 4 comments
  • libgkl_compression.so not found + Failed to detect Google Compute Engine in a GATK workflow Answered
    • Marta Giovalli
    • September 14, 2022 12:47
    • Edited
    0 votes 4 comments
  • Haploytpe caller shows me that 0 read(s) were filtered by: MappingQualityAvailableReadFilter etc. Answered
    • pb
    • July 13, 2022 14:15
    0 votes 4 comments
  • Refseq accession number and version number in Funcotator Answered
    • TMB
    • April 26, 2022 04:13
    0 votes 4 comments
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