Question: ancestry prediction from array data
gravatar for wes3985
3.6 years ago by
wes39850 wrote:

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 • 1.0k views
ADD COMMENTlink modified 3.6 years ago by WouterDeCoster44k • written 3.6 years ago by wes39850
gravatar for WouterDeCoster
3.6 years ago by
WouterDeCoster44k wrote:

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.

ADD COMMENTlink written 3.6 years ago by WouterDeCoster44k

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

ADD REPLYlink written 3.6 years ago by wes39850
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1633 users visited in the last hour