Perform Plink association tests on a genetype file with one allele

Question

[davidenoma]

Is there a way to perform genetic association tests for a genotype file which has only one allele at each position? For example:

Chromosome,Positions,6114,6111,6108,
1,657,T,C,T,

The phenotype file is also available as well.

Answer 1

[LChart]

All variants in plink need to be bi-allelic. You can look up the reference allele in the appropriate reference fasta and use that to re-encode the variant map.

If you're asking about a haploid/monoploid species, you can use --chr-set to control ploidy settings.

[davidenoma]

Thanks for the suggestion. I think it makes sense. Is there code already available to convert it the format which post or I have to custom write it?