Question: Ancestral allele in VCF files
gravatar for thjnant
5.9 years ago by
thjnant100 wrote:


I have been using the --derived option in vcftools to obtain the frequency of the ancestral and derived allele in africa, america, europe and asia of the 1000 Genomes project. 

What I was expecting to get was an equal number of SNPs with ancestry information, however, I get different number of SNPs for different continents that the ancestry information is available to them. 

I cannot figure out how this can happen. Any insight would be appreciated.

Thank you very much in advance.

vcftools • 2.6k views
ADD COMMENTlink modified 5.8 years ago by Biostar ♦♦ 20 • written 5.9 years ago by thjnant100
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