#!/bin/bash

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###Fabio Morgante
###11-2-2016
###Simulation of one chromosome arm
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####Simulation of 10,000 haplotypes of 1 Mb, -s seed, theta = 0.04, rho = 0.04 
./macs 10000 5e06 -s 120 -t 0.04 -r 0.04 -h 1e3 | ./msformatter > haplo_arm1.txt

####Once the haplotypes have been simulated, just duplicate them to make chromosomes
####for diploid inbred individuals. Then, convert to preferred format (e.g. plink format 
####or additive code). The other two arms followed the same procedure but with different seed 
####(125 for arm2, and 130 for arm3).