Intersect phenotype and covariate files to get total N from each phenotype file.

get_ns.r

for file in $(ls pheno | grep .pheno)
do
 fname=$(echo $file | awk 'BEGIN {FS="_"}{print $2}')
 fname2=$(echo $file | awk 'BEGIN {FS="_"}{print $3}' | sed 's/.pheno//g')
 
# scount=$(awk '{print $3}' pheno/$file | grep -v NA | wc -l | awk '{print $1}')
 scount=$(LC_ALL=C join <(awk '{print $1"_"$2,$3}' pheno/$file  | LC_ALL=C sort -k1b,1 ) <( awk '{print $1"_"$2}' pheno/p2_"$fname"_eur_"$fname2"_agesex.cov | LC_ALL=C sort -k1b,1) | awk '{print $2}' | grep -v NA | wc -l | awk '{print $1}')
 
 echo $fname $fname2 $scount 
 head -n1 pheno/$file
done