population stratification using PLINK

Question

[fatma.mokhtar]

Hello,

If I have a sample of individuals and I know that they are all from one city from one country, should I do population stratification using PLINK? if yes, which number after the --K should I write? I don't know how to cluster this? and for the MDS, which number should I use?

Is this the right command?

plink --bfile hapmap1_cleaned --read-genome hapmap1_genome.genome --cluster --k 2 --mds-plot 4 --out mds_example

Thank you in advance,

[Nicolas Rosewick]

did you plot the PCA to check if some outliers are within your cohort. Also you can maybe try https://github.com/brentp/peddy for pop strat.