A collection of scripts (1 to 9) used succesively to analyse the microhaplotype data from ~2000 individuals of Oncorhynchus mykiss from the Big Creek population in California. Parentage and sisbship analyses were performed, as well as power simulations to compare SNPs and microhaplotypes, spatial genetic structure analyses, and more !
The scripts require the initial VCF (or any VCF obtained from the raw data) as well as some metadata, all which will be put online upon the publication of the associated paper :)
Cheers Noé