eigenstrat smartpca input files

Question

[gulcek]

I want to apply eigenstrat's smartpca to 23andme raw snp datasets for 1500 people, there should be 3 input files to use smartpca : genotype file, individual file and snp file. In individual file I need to indicate indivudal's case or control label. how do I label each individual either case or control? My dataset does not have any case and control patients.

The example of individual file is in this link:

https://github.com/DReichLab/EIG/blob/master/EIGENSTRAT/example.ind

Answer 1

[rbagnall]

You don't have to label them as case and control, the program will still run and plots will be produced.

For example, I ran eigenstrat on exome data from the 1000 genomes project, and labelled the samples according to population (AFR, EUR, EAS or SAS)