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Old 01-20-2011, 05:10 AM   #2
aleidenroth
Junior Member
 
Location: Nottingham, UK

Join Date: Nov 2009
Posts: 8
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I have the same problem, I also use bwa -r for alignment.

When I re-run TableRecalibrate with the added parameter

--default_read_group name_of_my_read_group

it seems to work and ignores the unmapped reads. However, I'm not sure this will cause any trouble in downstream analysis?
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