Hello, as the title states I just need a little help fully understanding what the -split flag does in the bedtools utility, bamtobed. It states,
-split Report each portion of a “split” BAM (i.e., having an “N” CIGAR operation) alignment as a distinct BED intervals.
However, upon being asked about how this affects output I couldn't properly answer(It gives us expected results when used, when it is missing the results are wrong). I was wondering if someone could help me understand what exactly happens with this flag.