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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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  • Error in running SplitNCigarReads - htsjdk.samtools.util.RuntimeIOException Answered
    • KATHIE NGO
    • August 27, 2020 17:31
    • Edited
    0 votes 9 comments
  • Merge different individual VCF
    • Linda Do
    • July 06, 2020 07:05
    1 vote 13 comments
  • Issue with GenotypegVCFS after Genomics DB import, building vs updating
    • Melissa Spear
    • November 17, 2023 16:51
    • Edited
    0 votes 6 comments
  • Error when building an image using Dockerfile
    • E Ra
    • November 18, 2023 16:21
    0 votes 2 comments
  • GenomicsDBImport: An index is required, but none found with file ending .idx
    • Leo
    • November 16, 2023 22:41
    • Edited
    1 vote 1 comment
  • error for gatk -- PathSeqPipelineSpark "java: bwa.c:329: bwa_mem2idx: Assertion `k == l_mem' failed."
    • haha xixi
    • November 14, 2023 08:49
    • Edited
    1 vote 1 comment
  • PathSeq freezing
    • John Perkins
    • November 02, 2023 18:08
    • Edited
    0 votes 1 comment
  • GATK BQSR is taking too long to be run (running since last 6 days)
    • Niharika
    • November 07, 2023 05:10
    0 votes 1 comment
  • Error in running SplitNCigarReads - Attempt to add record to closed writer
    • Valerie Crolley
    • September 18, 2023 16:45
    0 votes 19 comments
  • Do I need to perform fastqc and adapters trimming before gatk pipeline?
    • LG
    • May 01, 2020 02:49
    2 votes 6 comments
  • GATK 4.4.0 Conda Environment Installation Error: ResolvePackageNotFound: - defaults::tensorflow=1.15.0
    • Stephen Harding
    • October 26, 2023 21:23
    • Edited
    0 votes 1 comment
  • string length error generated by funcotator while processing a mutect2 vcf
    • Robert Bremel
    • October 11, 2023 15:45
    0 votes 5 comments
  • Error in MutSigCV on GenePattern
    • HT Liu
    • September 03, 2023 15:06
    0 votes 1 comment
  • GenomicsDBImport: has too many genotypes in the combined VCF record
    • Nils Homer
    • August 06, 2020 00:12
    • Edited
    1 vote 4 comments
  • CombineGVCFs with error output
    • Yifei Sun
    • September 27, 2023 01:42
    0 votes 5 comments
  • ASEReadCounter output for Indels is incorrect
    • Akshay Zawar
    • September 21, 2023 11:36
    0 votes 1 comment
  • Error in GATK CollectAllelicCounts
    • Saloni Sinha
    • September 14, 2023 17:27
    0 votes 4 comments
  • PathSeqPipelineSpark multiple cpus
    • Caitlin Newman
    • September 12, 2023 16:39
    0 votes 1 comment
  • HaplotypeCaller - Shutting down engine - Encountering a large genome
    • zyw
    • December 07, 2020 02:27
    0 votes 7 comments
  • Liftover Picard hg19 to hg38: variants were not successfully lifted over Answered
    • Andres Caballero
    • December 09, 2022 18:39
    2 votes 3 comments
  • GATK Index Feature FIle No suitable codecs found Answered
    • Y R
    • August 29, 2023 15:32
    • Edited
    0 votes 4 comments
  • Install GATK version 4.1.0.0 using Conda. Answered
    • dongju
    • August 29, 2023 08:32
    0 votes 4 comments
  • BaseRecalibrator on MT .bam files Answered
    • Sharon Cox
    • February 19, 2021 09:48
    • Edited
    0 votes 5 comments
  • Out of memory error using OpenJDK vs Oracle JDK for CNV-LOH
    • Jose Arcadio Buendia
    • February 28, 2020 01:53
    • Edited
    2 votes 3 comments
  • problem with R library
    • Laurent MANCHON
    • June 21, 2023 09:38
    0 votes 4 comments
  • Could not find walker with name: DepthOfCoverage
    • Kayleigh Ostberg
    • August 21, 2023 15:11
    • Edited
    0 votes 1 comment
  • evaluation of the VCF file which is made using GATK Answered
    • behzad
    • June 22, 2020 11:41
    0 votes 6 comments
  • SplitNCigarReads does not seem to split reads properly as it was before 3.8-1?
    • SkyWarrior
    • June 21, 2021 13:29
    • Edited
    0 votes 9 comments
  • Haplotype caller taking too long
    • Rami Kheireddine
    • July 09, 2023 23:43
    0 votes 11 comments
  • User error: input files reference and features have incompatible contigs
    • mons7re
    • February 14, 2020 14:12
    0 votes 8 comments
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