genotyping
A variant site and alleles.
Discovers the variants present in a set of aligned reads.
Discovers the variants present in a set of aligned reads.
Useful for force-calling variants.
Jointly calls variants and computes variant annotations.
Squares off a set of genotypes with reference models.
Squares off a set of genotypes with reference models.
Many joint genotyping workflows use a "Genome VCF" (gVCF) based approach to incrementally compute genotype likelihoods across their dataset. In this methodology, we generate genotype likelihoods at all positions in all samples. For sites where we do not see evidence of a variant, we compute a "reference model", which is a set of genotype likelihoods assuming that we saw an unknown alternate allele. These likelihoods are then used in a joint genotyping step.
The alternative to this approach is to discover variants across all samples simultaneously, and to then score these variants. This approach is generally considered too computationally expensive for large cohorts.
This singleton object "squares off" the reference model by discovering all sites where we called a variant in at least one sample, joining these discovered variants back against the input genotypes, and then excising the genotype likelihoods from the reference models.
Variant caller for genotyping the offspring of two parents.
A variant site and alleles.
The contig this variant is on.
The position this variant starts at.
The reference allele this variant varies from.
The substituted allele.