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Old 02-02-2016, 12:00 PM   #1
Location: US

Join Date: May 2013
Posts: 31
Default Pileup file: base positions on reads

Why are there more base positions than nucleotide reads in a samtools pileup file generated using the -O argument (output base positions on reads)? I am trying to filter out reads at read ends and am confused by this format.

Thank you!
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Old 02-03-2016, 10:45 AM   #2
Rick Westerman
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104

Could you give us an example of a line that confuses you?
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