file1=~/local/vc_asthma.sim
rm $file1

seed=10001
while [ $seed -le 11000 ]
do	#1#


for i in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22;
  do	#2#


# First: Runs Merlin on the real dat, ped and map files and creates replicate dataset #
# (dat, ped and map files) with simulated genotypes under the null of no linkage #
merlin -d asthma_chr${i}.dat -p asthma_chr${i}.ped -m asthma_chr${i}.map --simulate --save -r $seed


# Second: runs linkage analysis identical to that used with real data but now on the replicate dat, ped and map files #
merlin -d merlin-replicate.dat -p merlin-replicate.ped -m merlin-replicate.map --grid:2 --start:0 --vc --usecovariates > temp.dat


# Third: Joins the output of all chromosomes and of all simulations #
cat temp.dat | tail +`grep -n "            Position      H2    ChiSq     LOD  pvalue" < temp.dat | awk -F ':' '{ print $1 }'` | tail +2 | grep -v "^$" | awk '{ print $0, '"$i"' }' | awk '{ print $0, '"$seed"' }' >> $file1


  done	#2#

seed=`expr $seed + 1`

done	#1#