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List of IBD / IBS values for all pairs

	./plink --file mydata --genome

which create the file

	plink.genome

Current output has columns:

	ID (family, individual) for individual 1 (2 cols)
	"X"
	ID (family, individual) for individual 2 (2 cols)
	P(IBD=0)
	P(IBD=1)
	P(IBD=2)
	pi-hat = proportion of alleles shared IBD = P(IBD1)/2 + P(IBD2) 
	Number of IBS 0 loci
	Number of IBS 1 loci 
	Number of IBS 2 loci

Therefore,

	sort -nr --key=9 plink.genome | head -n 50

or something similar is a good way of getting the top 50 most relateds. I would advocate also calculating the average pi-hat for each individual and looking for outliers: indicative of true relationships, and sample contamination (i.e. too many hets -> fewer IBS 0 calls -> over-estimated IBD with all other people in the sample).

HETEROZYGOSITY

	./plink --file mydata --inbreeding

Output is in

	plink.het

and contains the fields

	Family ID
	Individual ID
	# observed homozygous genotypes
	# expected homozygous genotypes
	# non-missing genotypes
	F inbreeding coefficient

Remember to do this only for autosomal markers: this can be achieved by having a MAP file with the X/Y markers with 0's in the 4th column to exclude them. [note: set to automatically exclude these] [an error occurred while processing this directive]