Converting Affymtrix SNP data to plink and VCF formats

Question

[robjohn70000]

Hi,

I have a raw Affymtrix SNP data that I will like to convert to Plink and VCF formats. The columns of my data are as follows:

"Probe ID","Affy SNP ID", "dbSNP RS ID","Chromosome","Physical Position","Position End","Strand","ChrX", "Allele A","Allele B","Ref Allele","Alt Allele"  etc.

I'm new to genetics and gwas analysis. Can someone please advise me on what to do.

Answer 1

[Kevin Blighe]

Greetings to Nigeria.

As this is Affymetrix genotyping data, you can use Affymetrix Power Tools to convert to either VCF or PLINK. Take a look HERE.

Good luck,

Kevin

[robjohn70000]

Thanks so much for the info @Kevin Blighe.