Entering edit mode
7.4 years ago
wes3985
▴
10
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?
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