Question: pileup vs. IGV insertion locations
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gravatar for blur
2.1 years ago by
blur110
European Union
blur110 wrote:

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,

igv pileup • 573 views
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