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Methods and Algorithms
Reasoning and analytical details behind the tools
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)