check relatedness of individuals
I used 1000 g data sets to simulate the sequence. After performing simulation, I got 10K individuals, for some other analyses. I wonder, how i can check the relatedness of simulated individuals with original data (individuals)? Should I first calculate simple correlation of MAF from two data sets or any other method? My both data sets are in PLINK format. Any suggestion please?
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Merge both data. Throw away SNPs with MAF<=5%,
remove SNPs in LD (pairwise ). Use KING for kinship. One should have ~40-60-90K SNPs usually to find kinship.Edit: 06/21/2018
~20K SNPs are good too to infer kinship. http://people.virginia.edu/~wc9c/KING/Download.htm
Also, it's suggested not to prune good SNPs at http://people.virginia.edu/~wc9c/KING/manual.html