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4_calculate_LD.md

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./scripts/4_calculate_LD.sh

All commands to be run in the terminal.

See Plink documentation here.

For each of the six poulations, use Plink to calculate LD between each pair of loci. The "--r2 square" flag to Plink will produce a LxL matrix of pairwise r2, with L as the number of loci.

plink --bfile ./work/Koppen_ODD --r2 square --out ./work/Koppen_ODD

plink --bfile ./work/Koppen_EVEN --r2 square --out ./work/Koppen_EVEN

plink --bfile ./work/Nome_ODD --r2 square --out ./work/Nome_ODD

plink --bfile ./work/Nome_EVEN --r2 square --out ./work/Nome_EVEN

plink --bfile ./work/Puget_ODD --r2 square --out ./work/Puget_ODD

plink --bfile ./work/Puget_EVEN --r2 square --out ./work/Puget_EVEN