Question: Phased genotype hapmap3 data encoded as 0 1.
1
gravatar for nastasia
12 months ago by
nastasia10
nastasia10 wrote:

Dear Community,

I would like to use GWAsimulator to simulate GWAS data for different populations. This tool consider only phased data as input. Each row is a phased chromosome with bi allelic SNP, each allele coded as 0 or 1.

I choosed to simulate data using Hapmap3 for YRI population as input:

ftp://ftp.ncbi.nlm.nih.gov/hapmap/genotypes/2010-05_phaseIII/hapmap_format/consensus/

But, it is coded as A C G T and not as 0 1.

Do you know how can I convert it to 0 1 encoding? What package do I need to use? Otherwise, there are also the plink files format in the hapmap website,, can I convert ped file to hap file?

Thanks in advance for your suggestions.

hapmap3 snp plink gwas • 309 views
ADD COMMENTlink modified 10 months ago by Biostar ♦♦ 20 • written 12 months ago by nastasia10
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