Question: Converting Affymtrix SNP data to plink and VCF formats
0
gravatar for robjohn70000
2.5 years ago by
robjohn70000130
Nigeria
robjohn70000130 wrote:

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.

affymetrix plink snp gwas vcf • 1.2k views
ADD COMMENTlink modified 21 months ago by Biostar ♦♦ 20 • written 2.5 years ago by robjohn70000130
1
gravatar for Kevin Blighe
2.5 years ago by
Kevin Blighe65k
Kevin Blighe65k wrote:

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

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by Kevin Blighe65k

Thanks so much for the info @Kevin Blighe.

ADD REPLYlink written 2.5 years ago by robjohn70000130
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