Algorithms
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Structural variant (SV) discovery
In this article, you'll learn how to identify structural variants in one or m... -
ActiveRegion determination (HaplotypeCaller and Mutect2)
This document details the procedure used by HaplotypeCaller to define ActiveR... -
Evaluating the evidence for haplotypes and variant alleles (HaplotypeCaller and Mutect2)
This document details the procedure used by HaplotypeCaller to evaluate the e... -
Local re-assembly and haplotype determination (HaplotypeCaller and Mutect2)
This document details the procedure used by HaplotypeCaller to re-assemble re... -
Allele-specific annotation and filtering of germline short variants
Overview The traditional VQSR recalibration paradigm evaluates each position... -
Variant Quality Score Recalibration (VQSR)
VQSR stands for Variant Quality Score Recalibration. In a nutshell, it is a s... -
Evaluating the quality of a germline short variant callset
The germline short variant discovery pipeline produces a variant callset in t... -
HaplotypeCaller Reference Confidence Model (GVCF mode)
This document describes the reference confidence model applied by HaplotypeCa... -
Base Quality Score Recalibration (BQSR)
BQSR stands for Base Quality Score Recalibration. In a nutshell, it is a data... -
After gCNV calling considerations
The Germline CNV (gCNV) workflow tutorial is available here. The tutorial lay... -
Assigning per-sample genotypes (HaplotypeCaller)
This document describes the procedure used by HaplotypeCaller to assign genot... -
Genotype Refinement workflow for germline short variants
Contents Overview Summary of workflow steps Output annotations Example More... -
Somatic calling is NOT simply a difference between two callsets
To better understand what somatic calling entails, we contrast it to germline... -
HaplotypeCaller in a nutshell
This document outlines the basic operation of the HaplotypeCaller run in its ... -
Difference between QUAL and GQ annotations in germline variant calling
It seems people often get confused about the difference between QUAL and GQ, ... -
Hard-filtering germline short variants
This document aims to provide some insight into the logic of the generic hard... -
Calculation of PL and GQ by HaplotypeCaller and GenotypeGVCFs
PL is a sample-level annotation calculated by HaplotypeCaller and GenotypeGVC... -
The logic of joint calling for germline short variants
Better together For germline short variants (SNPs and indels), we recommend ... -
Calling variants on cohorts of samples using the HaplotypeCaller in GVCF mode
This document describes the new approach to joint variant discovery that is a...