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

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)?

genotypes vcf
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written by Jeremy Leipzig Jeremy Leipzig

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

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written by GenoMax GenoMax

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

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written by Jeremy Leipzig Jeremy Leipzig

1 answer

Numeric bialleles and nucleotide bialleles may be options.

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written by GenoMax GenoMax

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 :)

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written by cmdcolin cmdcolin

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)

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written by Jeremy Leipzig Jeremy Leipzig

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