Technical Documentation
Troubleshooting GATK4 Issues
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How to setup and use temporary folder for GATK local execution
GATK tools like many other bioinformatics software rely on temporary files cr... -
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...
Glossary
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Structural Variants
Structural variants are key players in human evolution and disease, but they ... -
How to interpret SV VCFs
Introduction The GATK-SV pipeline outputs structural variant records in VCF ... -
Functional equivalence in DRAGEN-GATK
DRAGEN-GATK is an open-source, GATK-based pipeline that aims to produce resul... -
Reference Genome Components
This document defines several components of a reference genome. We use the ... -
GATKReport and gsalib
A GATKReport is simply a text document that contains well-formatted, easy to ... -
Fisher’s Exact Test
Overview Fisher’s Exact Test is a statistical test that is used to analyze c...
Algorithms
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Structural variant (SV) discovery
In this article, you'll learn how to identify structural variants in one or m... -
ActiveRegion determination (HaplotypeCaller and Mutect2)
This document details the procedure used by HaplotypeCaller to define ActiveR... -
Evaluating the evidence for haplotypes and variant alleles (HaplotypeCaller and Mutect2)
This document details the procedure used by HaplotypeCaller to evaluate the e... -
Local re-assembly and haplotype determination (HaplotypeCaller and Mutect2)
This document details the procedure used by HaplotypeCaller to re-assemble re... -
Allele-specific annotation and filtering of germline short variants
Overview The traditional VQSR recalibration paradigm evaluates each position... -
Variant Quality Score Recalibration (VQSR)
VQSR stands for Variant Quality Score Recalibration. In a nutshell, it is a s...
Note that the information in this documentation guide is targeted at end-users. For developers, the source code and related resources are available on GitHub.