if [ $# = 0 ]; then
    echo "Usage: do-prune.sh PLINKBASE  "
    echo "       do-prune.sh PLINKBASE rsqdval"
    echo
    echo "       PLINKBASE is base name for plink bed/bim/fam file"
    echo "       default rsqdvalue is 0.2"
    exit 0;
fi
if [ $# = 1 ]; then
    R2=0.2
else
    R2=$2
fi


F=`basename $1`

plink --allow-no-sex --bfile $1 --indep-pairwise 50 10 $R2 --out /tmp/$F
plink --allow-no-sex --bfile $1 --extract /tmp/$F.prune.in --make-bed --out $F-prune