conversion of genotyping data to VCF format

Question

[theoharis]

Hi

Ive genotyping data in this format:

rs10010131 A A

ie SNP allele1 allele2

Is there an off the shelf tool I can use to convert to VCF?

Answer 1

[S. Roa]

Hello, Theo!

A very famous and useful is Plink: https://zzz.bwh.harvard.edu/plink/

[caleb_dume]

Something to keep in mind if using plink 1.90 for this conversion: Why would you need to specify `--keep-allele-order` and `--a2-allele` when writing a VCF with PLINK?

Otherwise the ref allele in your vcf will automatically be set to the major allele from your genotype data which may not be what you want.