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perl -alnF"\t" -e 'if($#F==2){$F[3]=$F[2];$F[2]="NA";print "@F"} else {print "@F"}' input_file

Try this if its given that always third column value is missing and 4th column is third column.

I got the below


$ perl -alnF"\t" -e 'for($i=0;$i<=$#F;$i++){ if(!$F[$i]){$F[$i]="NA";}} print "@F"' file4
ch:12 1 3 4
ch:13 3 3 4
ch:25 1 NA 8
ch:23 2 8 1


Input :

ch:12^I1^I3^I4$...

perl -alnF"\t" -e 'for($i=0;$i<=$#F;$i++){ if(!$F[$i]){$F[$i]="NA";}} print "@F"' input_fiile