English terms distinguishing genotype allelic nucleotides (T/C) from VCF encoded genotype (0/1)

Question

[Jeremy Leipzig]

In English what would you call the combination of alleles that occur at a position in a sample if they are represented by actual nucleotide (e.g. T/C)?

OK, then what would you call them if they are represented by encoded digits where 0 is reference, as seen in VCFs (e.g. 0/1)?

[GenoMax]

Not sure if you are looking for a single word/term but to keep things simple: Nucleotide encoded alleles vs binary encoded alleles.

[Jeremy Leipzig]

maybe "integer-encoded bialleles" or "integer-encoded genotype". i can't say these really roll off the tongue.

Answer 1

[GenoMax]

Numeric bialleles and nucleotide bialleles may be options.

[Jeremy Leipzig]

I approve of these

[cmdcolin]

not sure if 'bi' is short for binary here, but note that in VCF, the genotypes are not always binary. it is an integer index into the ALT field, so if there are several alts it can be like 3/4. and of course, it's not always diploid either :)

[Jeremy Leipzig]

biallelic refers to diploid here, not the number of observed alts in a population

numeric monoalleles or nucleotide monoalleles would be on chrY for example

(but I do get what you are saying, since people talk about decomposing multiallelic variants)