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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 all All Planned Not planned Completed Answered No status Sort by comments Newest post Recent activity Votes Comments
  • Interval Filtering -- How does it actually work?
    • Alijah O'Connor
    • September 21, 2020 22:54
    • Edited
    0 votes 4 comments
  • Picard CollectHsMetrics PCT_EXC_OFF_TARGET
    • Holly Corbitt
    • May 07, 2020 04:09
    1 vote 4 comments
  • A USER ERROR has occurred: Number of read groups must be >= 1, but is 0
    • Jay Singh
    • May 01, 2020 17:24
    0 votes 4 comments
  • Do I need to perform fastqc and adapters trimming before gatk pipeline?
    • LG
    • May 01, 2020 02:49
    1 vote 4 comments
  • ValidateSamFile tmp not found ERROR with not output or Exception
    • James
    • April 20, 2020 23:34
    0 votes 4 comments
  • Picard ExtractIlluminaBarcodes return NullPointerException error
    • Jing Lin
    • March 20, 2020 21:52
    0 votes 4 comments
  • Do BQSR ignore VCF sites marked as filtered, or must they be removed from the file?
    • mk
    • March 11, 2020 00:37
    0 votes 4 comments
  • Question: Picard - MergeBamAlignment: Reads remaining on alignment iterator
    • Nguyen Nguyen Thanh
    • February 23, 2020 15:03
    0 votes 4 comments
  • HaplotypeCaller produces very large .idx files
    • Anze Staric
    • February 20, 2020 20:30
    1 vote 4 comments
  • WES covarage analysis
    • Surdan Burasi
    • February 16, 2020 21:09
    0 votes 4 comments
  • GATK R plots with R v4.1.2 Answered
    • Franz Gassner
    • January 24, 2022 09:36
    0 votes 3 comments
  • MarkduplicatesSpark failed Answered
    • lid.zigh
    • November 23, 2021 13:44
    0 votes 3 comments
  • markduplicatesSpark .bam.parts output error (directory already exists) Answered
    • Morgan Sparks
    • September 30, 2021 16:31
    0 votes 3 comments
  • GenomeSTRiP SVPreprocess failed Answered
    • Jenny Xu
    • July 27, 2021 02:46
    0 votes 3 comments
  • LiftoverVcf: hg19 to hg38 all variants mismatched
    • Ken Hanscombe
    • February 17, 2021 14:13
    0 votes 3 comments
  • How to work with CNN variant caller
    • Danio Rerio
    • February 16, 2021 16:09
    0 votes 3 comments
  • Mitochondrial analysis - FilterMutectCalls autosomal-coverage is not an option Answered
    • leory
    • February 16, 2021 13:42
    0 votes 3 comments
  • Cromwell stuck at WaitingForReturnCode on Mac
    • Marc Crepeau
    • February 01, 2021 21:00
    0 votes 3 comments
  • Why do I see difference in ploidy in GT field within same sample after GenotypeVCFs
    • Emila Mańko
    • January 21, 2021 17:54
    0 votes 3 comments
  • ASEReadCounter java.lang.ArrayIndexOutOfBoundsException: 0
    • zhaol
    • January 08, 2021 07:38
    0 votes 3 comments
  • BQSR no output table found
    • Tamrin Chowdhury
    • December 17, 2020 07:20
    0 votes 3 comments
  • Errors with CNNScoreVariants and HaplotypeCaller: java.nio.BufferUnderflowException
    • WKaiser
    • December 03, 2020 16:11
    0 votes 3 comments
  • PathSeq Generate K-mer Library
    • DeLuca Lab
    • November 16, 2020 16:46
    0 votes 3 comments
  • erro NativeGenomicsDB - pid=26649 tid=26687 conflicting field description in the vid JSON and the VCF header of file:
    • Hind Fakhri
    • October 08, 2020 08:43
    0 votes 3 comments
  • PathSeq output
    • Arman Ardalan
    • August 18, 2020 07:49
    0 votes 3 comments
  • Error: Invalid or corrupt jarfile cromwell-52.jar
    • Saatvig Patel
    • July 27, 2020 10:07
    0 votes 3 comments
  • Unable to load library 'lsf': liblsf.so: and Unable to submit job: denied(CNVdiscovery)
    • termius
    • July 19, 2020 14:40
    0 votes 3 comments
  • Warning: Reading will be unbuffered. Answered
    • Linda Do
    • July 06, 2020 16:35
    1 vote 3 comments
  • SelectVariants to get a vcf file with 1 individual from a vcf file with 3 individuals
    • Linda Do
    • June 22, 2020 21:46
    0 votes 3 comments
  • Picard LiftOverVCF 2.22.3. hs37d5_to_GRCh38. Many mismatched reference alleles
    • Argonaut44
    • June 23, 2020 18:09
    • Edited
    0 votes 3 comments
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