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Old 09-19-2013, 10:13 PM   #2
BAMseek
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Location: St. Louis, MO, USA

Join Date: Apr 2011
Posts: 124
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Hey Eric,

My guess would be that if a read is split (such as spanning a splice junction), then that read may count towards the coverage for the entire interval, even the skipped bases. This link seems to talk about a similar issue. Looks like the solution in the post is to split those reads and try coverage again.

(Edit: although looks like you did use the -split argument so maybe it is a different issue).

Justin

Last edited by BAMseek; 09-19-2013 at 10:16 PM.
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