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for study in brya ftca gsdc mrsc nhrv nhs2 nss1 nss2 onga pts1 psy2 psy3 
do
 #cat "$study"/infoeur/*.dosage | awk '{if(NR == 1 || ($1 != "CHR" && $6 > 0 && $6 < 1)) print $2,$1,$3,$4,$5,$6,$7}' >  "$study".mafinfo
 cat "$study"/infoeur/*.dosage | awk '{if(NR == 1 || ($1 != "CHR" && $6 > 0 && $6 < 1)) print $2,$4,$5,$6,$7}' | LC_ALL=C sort -k1b,1 >  "$study".mafinfo
done

#Note: Assumes that the SNP is the first column of your gwas results file. If it is not, change "sort k1b,1" 
to the column number where the SNP is. e.g. if SNP is in column 2, change to sort k2b,2 gwas_results.assoc.txt 

LC_ALL=C join <(LC_ALL=C sort k1b,1 "$study"_gwas_results.assoc.linear) "$study".mafinfo > "$study"_results_withmaf.txt