In SAM file, the CIGAR string has the following options:
op Description M Alignment match (can be a sequence match or mismatch I Insertion to the reference D Deletion from the reference N Skipped region from the reference S Soft clip on the read (clipped sequence present in <seq>) H Hard clip on the read (clipped sequence NOT present in <seq>) P Padding (silent deletion from the padded reference sequence) `
I can not tell the difference between 'D' and 'N' when I analyze split read mapping. could someone give me an example to illustrate the difference?
Can you show a CIGAR string of such type you encountered??