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ancestry prediction from array data

What is the best way to work out ancestry from array data such as this:

    Sample ID   SNP Name    Chr Position    Allele1 - Top   Allele2 - Top   B Allele Freq   Log R Ratio
7512498063_R04C01   rs2661837   6   160790174   C   C   0.0000  0.0863
7512498063_R04C01   rs17599091  4   100512919   G   G   1.0000  0.2737
7512498063_R04C01   rs1492138   12  22030178    A   A   0.0000  -0.0156
7512498063_R04C01   rs7774255   6   29274356    T   T   1.0000  0.0612
7512498063_R04C01   rs206018    6   32177880    G   G   0.9890  0.2482
7512498063_R04C01   rs11929668  3   119535795   G   G   0.9837  -0.0526
7512498063_R04C01   rs4252072   6   161128264   A   A   0.0000  -0.1592

Are there tools available to work out where each SNP is most common and therefore predict ancestry?

snp ancestry
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updated by WouterDeCoster WouterDeCoster • written by wes3985 • wes3985

1 answer

I think peddy comes close to what you are looking for, not sure how many SNPs you have and therefore if it's truly applicable.

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written by WouterDeCoster WouterDeCoster

Thanks for the suggestion. The data is from arrays, so about 2.3 million SNPs. The only problem is peddy seems to take a vcf file and my data is in the format above so I would need another tools to convert? Are you aware of any? Thanks again

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written by wes3985 • wes3985

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