You can play with bash commands..

I don't remember the column that represents the CIGAR (I believe is column 7)

You can do the following

cat your_file.sam | cut -f 7 | grep "N" | wc -l

If playing with BAM files

samtools view your_file.bam | cut -f 7 | grep "N" | wc -l

With cat and samtools view you open the content of the file and pipe it to the cut command, which select column 7. With grep you select those lanes containing a N into the CIGAR string, and pipe it again to wc -l which count the lanes containing such a N