Hello all,
I wish to determine pairwise relatedness and eventually reconstruct pedigrees for a population of dolphins using high-density microsatellites (>2000 loci/individual). However, most genome-wide estimators of IBD are optimized for SNPs. Is anyone aware of a program that can compute IBD/kinship coefficients from multiallelic genome sequence data? Alternately, does anyone have experience entering microsats into PLINK or KING?
Ideally I would like to be able to use a program like PRIMUS or CLAPPER to reconstruct pedigrees.
Hi
In one way, you can regress the population pairwise FST and RST against the log10 value of the geographical distances between your studied populations.
Good luck
Look at the software provided by Wang. https://www.zsl.org/science/users/jinliang-wang
COANCESTRY would probably be the one you want.
I would suggest you to check Identix which propose several relatedness indicators based on microsatellites. I do think the number of markers you have would be a problem. (https://pdfs.semanticscholar.org/a4da/a6d166a6b4ddb33c479d3981d3b925a5bf24.pdf)
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