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...