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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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  3. Troubleshooting GATK4 Issues

Troubleshooting GATK4 Issues

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  • Troubleshooting GATK-SV
    The GATK-SV pipeline was built and is meant to be used on the Terra platform....
  • Known Issue with Funcotator Germline v1.6 Data Sources
    There is a known issue with the Funcotator germline v1.6 data resources. For ...
  • GenomicsDBImport usage and performance guidelines
    This document contains information on the best practices and guidelines to fo...
  • Known Issue with CNNScoreVariants version 4.1.9.0
    There is a known issue with CNNScoreVariants and the conda environment in the...
  • When HaplotypeCaller and Mutect2 do not call an expected variant
    You may find, after running an analysis with HaplotypeCaller or Mutect2, that...
  • Missing physical phasing information in vcf?
    The way the phasing algorithm decides to phase is by checking whether two var...
  • I am unable to use VQSR (recalibration) to filter variants
    The problem: In order to filter variants after the calling step, we prefer t...
  • Exception in thread main java lang NoClassDefFoundError org xerial snappy LoadSnappy
    This can happen when you run GATK directly from the jar instead of using the ...
  • Errors in SAM or BAM files can be diagnosed with ValidateSamFile
    The problem You're trying to run a GATK or Picard tool that operates on a SA...
  • Need to run programs that require different versions of Java
    The problem We sometimes need to be able to use multiple versions of Java on...
  • VariantFiltration FT tag
    If the genotype filter was applied to at least one of samples only then the F...
  • Can't use VQSR on non-model organism or small dataset
    The problem: Our preferred method for filtering variants after the calling s...
  • SelectVariants Cookbook
    How to use SelectVariants to find common variants: gatk SelectVariants \ ...
  • Java is using too many resources (threads, memory or CPU)
    Most resource allocation problems you run into will be associated with either...
  • Errors about read group (RG) information
    See the Glossary entry on read groups for more information about what they re...
  • Java version issues
    As documented here, GATK requires a particular major version of Java. If you ...
  • Errors about misencoded quality scores
    The problem You get an error like this: SAM/BAM/CRAM file <filename> ...
  • Errors about input files having missing or incompatible contigs
    These errors occur when the names or sizes of contigs don't match between inp...
  • missing physical phasing information in vcf?
    The way the phasing algorithm decides to phase is by checking whether two var...
  • Expected variant at a specific site was not called
    This can happen when you expect a call to be made based on the output of othe...
  • Missing annotations in the output callset VCF
    The problem You specified -A <some annotation> in a command line invoking on...
  • Allele Depth (AD) is lower than expected
    The problem: My DP and AD values don't match up! Here's a common problem — Y...
  • Known Issues with Mutect2 GATK4.1
    Error: java.lang.IllegalArgumentException: log10p: Log10-probability must b...
  • Errors about contigs in BAM or VCF files not being properly ordered or sorted
    This is not as common as the "wrong reference build" problem, but it still po...
  • Deep sequencing data is missing variants in M2 called vcf
    --max-reads-per-alignment-start is helpful because the genome has a few hotsp...
  • Known Issues with VariantRecalibrator
    The syntax for specifying argument tags has changed (and the documentation wa...

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