Ancestral allele in VCF files
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6.8 years ago
thjnant ▴ 130

Hello, 

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 • 2.8k views
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