I have downloaded the 20101123 version RAW genotypes data encoded in VCF format. And I want to use plink to calculate the LD relation with my snp list.
The vcftools offered us a method to convert the vcf genotypes to plink ped format while not provide a method to extract one population data.
The VCFtoped perl script offered by 1000G can not extract all the chr data just within a defined region, and besides the info file is something different with the .map file of plink, missing chr column.
So is there any existing method to extract all genotypes in VCF format of CEU population?
If you know such a method, could you tell me how?
Best for all!