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Old 08-22-2013, 05:20 AM   #1
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Join Date: Aug 2011
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Default Post-alignment processing question

Hi all,

I have a question about doing the indel realinging and base quality recalibration steps after the initial alignments. Basically, Does it matter the order in which these are done? Can base recalibration be done before the indel realignment? Should it really matter?
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