two Queries A specific column of which has the same value sort -k $col1 $input1 > $input1.tmp; sort -k $col2 $input2 > $input2.tmp; join -1 $col1 -2 $col2 $input1.tmp $input2.tmp | tr " " "\t" > $out_file1; rm -rf $input1.tmp $input2.tmp