Heterozygous types in VCF

Question

[m.lee]

I'm working on encoding variant types in a VCF so that each variant has a single entry i.e. 0|0 becomes homozygous_ref and 1|1 becomes homozygous_alt.

I've not seen heterozygous variants subclassed into whether one allele is reference or not and wondered if this information is significant for a model that might be fitted to the categorised data. Are there cases where there is likely to be a significant difference between 0|1 variants and 1|2 variants e.g. in tumour suppression?

Thanks in advance for any answers/opinions

Matt

Answer 1

[Jorge Amigo]

The reference allele is an arbitrary nomenclature which the VCF format must use, therefore the only important thing for your model should be the alleles found at each particular position of the genome.