Methods and Algorithms

IMPORTANT: This is the legacy GATK documentation. This information is only valid until Dec 31st 2019. For latest documentation and forum click here

About Methods and Workflows

ActiveRegion determination HaplotypeCaller Mutect2

After gCNV calling considerations

Allelespecific annotation and filtering

Allelespecific annotation and filtering of germline short variants

Assigning persample genotypes HaplotypeCaller

Base Quality Score Recalibration BQSR

Base Quality Score Recalibration BQSR

Best Practices for Variant Discovery in DNAseq

Best Practices for Variant Discovery in RNAseq

Calculation of PL and GQ by HaplotypeCaller and GenotypeGVCFs

Calling variants in RNAseq

Combining variants from different files into one

Difference between QUAL and GQ annotations in germline variant calling

Evaluating the evidence for haplotypes and variant alleles HaplotypeCaller Mutect2

Evaluating the quality of a germline short variant callset

Evaluating the quality of a variant callset

Genotype Refinement workflow

Genotype Refinement workflow for germline short variants

Genotype Refinement workflow mathematical details

HaplotypeCaller in a nutshell

HaplotypeCaller Reference Confidence Model GVCF mode

Hardfiltering germline short variants

HC overview How the HaplotypeCaller works

HC step 1 Defining ActiveRegions by measuring data entropy

HC step 2 Local reassembly and haplotype determination

HC step 3 Evaluating the evidence for haplotypes and variant alleles

HC step 4 Assigning persample genotypes

How the HaplotypeCallers reference confidence model works

Introduction to the GATK Best Practices workflows

Local Realignment around Indels

Local reassembly and haplotype determination HaplotypeCaller Mutect2

Math notes How PL is calculated in HaplotypeCaller

Math notes Understanding the QUAL score and its limitations

Performing sequence coverage analysis

Purpose and operation of Readbacked Phasing

Reference implementation PairedEndSingleSampleWf pipeline

Selecting variants of interest from a callset

Somatic calling is NOT simply a difference between two callsets

The logic of joint calling for germline short variants

Understanding and adapting the generic hardfiltering recommendations

Using depth of coverage metrics for variant evaluation

Using JEXL to apply hard filters or select variants based on annotation values

Variant Quality Score Recalibration VQSR

Variant Quality Score Recalibration VQSR

VariantEval Evaluation Modules Glossary