Genotype track
The Genotype track (
) uses concepts similar to those in the VCF specification to facilitate import and export of the commonly used format (https://samtools.github.io/hts-specs/VCFv4.3.pdf).
Genotype tracks exist in either sample or database form, corresponding to VCF files with or without the FORMAT column, respectively.
Databases such as ClinVar, dbSNP, and Cosmic are usually made available in VCFs without the FORMAT and sample specific columns. Database variants are without genome context, in the sense that it varies from sample to sample if they are heterozygous or homozygous and which alleles at other loci they form haplotypes with. These variants are also referred to as conceptual variants, and the annotations they posses (VCF INFO column) are typically database or population specific as opposed to specific for a single sample.
Sample Genotype tracks describe the genome of a single sample. Sample variants can have both database and sample specific annotations and genome context is provided in genotypes and haplotypes.
Subsections