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
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 for germline short variants
Genotype Refinement workflow mathematical details
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