population stratification using PLINK
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,
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fatma.mokhtar •
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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.