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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]
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