Methods and Algorithms

Reasoning and analytical details behind the tools

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ActiveRegion determination (HaplotypeCaller & Mutect2)

After gCNV calling considerations

Allele-specific annotation and filtering of germline short variants

Assigning per-sample genotypes (HaplotypeCaller)

Base Quality Score Recalibration (BQSR)

Calculation of PL and GQ by HaplotypeCaller and GenotypeGVCFs

Calling variants on cohorts of samples using the HaplotypeCaller in GVCF mode

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

Genotype Refinement workflow for germline short variants

HaplotypeCaller Reference Confidence Model (GVCF mode)

HaplotypeCaller in a nutshell

Hard-filtering germline short variants

Local re-assembly and haplotype determination (HaplotypeCaller & Mutect2)

Somatic calling is NOT simply a difference between two callsets

The logic of joint calling for germline short variants

Variant Quality Score Recalibration (VQSR)