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-k1,1 tells sort that: first sort the file alphabetically using column 1 as the key. (1,1) means only use the first column.
The option just "-k1" would mean use the whole line as key starting with...

using shell script:

make a shell script (shell.sh) which takes 1 argument (data filename)

count=0
for i in `cat $1`
do
count=`expr $count + 1`
if [ $count -eq 1 ]
then
top=$i
fi
echo $i...

Using awk
If you just want to replace the . in the 3rd column

awk '{if($3==".") print $1" "$2" NA";else print}' infile