simulate phenotypes

simphen.sh

#!/bin/bash

# name of binary plink filename (excluding .bed/.bim/.fam suffix)
plinkfile=""

# output filename
outname=""

# number of causal variants
nvar=1000

# simulated h2
h2=0.8

# number of simulations
nsim=10


# Get random set of SNPs

shuf -n ${nvar} ${plinkfile}.bim | awk '{ print $2 }' > ${outname}.selectedsnps


# Use gcta to simulate some phenotypes

gcta64 \
	--bfile ${plinkfile} \
	--simu-qt \
	--simu-causal-loci ${outname}.selectedsnps \
	--simu-hsq ${h2} \
	--simu-rep ${nsim} \
	--out ${outname}