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.
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Viz •
1 answer
if you have a cigar string like this: 10M100N20M : the tool will break your record in two lines; one bed line of 10 bases (10M) and another one of 20 bases (20M), ignoring the 'intron' of 100 bp
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