Hi,

I am trying to parse a pileup file, so that for each nucleotide I'll have the number of non-ref vs. ref I wrote a script for that, but am having a problem understanding how to count insertions; it looks like that if the pileup looks like this: A 5 aaaa+TTT T 6 ,,,,,,

Then the IGV image shows the insertion is actually in the T position (the one after the position this +TTT appears on). So - how should I count the insertion? for A or T? Thanks in advance,