Methods and Algorithms

Analysis details and recommendations

About "Methods and Workflows"
Allele-specific annotation and filtering
Base Quality Score Recalibration (BQSR)
Best Practices for Variant Discovery in DNAseq
Best Practices for Variant Discovery in RNAseq
Calling variants in RNAseq
Calling variants on cohorts of samples using the HaplotypeCaller in GVCF mode
Combining variants from different files into one
Evaluating the quality of a variant callset
Genotype Refinement workflow
Genotype Refinement workflow: mathematical details
HC overview: How the HaplotypeCaller works
HC step 1: Defining ActiveRegions by measuring data entropy
HC step 2: Local re-assembly and haplotype determination
HC step 3 : Evaluating the evidence for haplotypes and variant alleles
HC step 4: Assigning per-sample genotypes
How the HaplotypeCaller's reference confidence model works
Introduction to the GATK Best Practices workflows
Local Realignment around Indels
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 Read-backed Phasing
Reference implementation: PairedEndSingleSampleWf pipeline
Selecting variants of interest from a callset
Understanding and adapting the generic hard-filtering recommendations
Using JEXL to apply hard filters or select variants based on annotation values
Using depth of coverage metrics for variant evaluation
Variant Quality Score Recalibration (VQSR)
VariantEval Evaluation Modules Glossary