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Old 10-25-2010, 09:57 PM   #6
Nils Homer
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Location: Boston, MA, USA

Join Date: Nov 2008
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Originally Posted by unagaswamy View Post
Hi Experts,
Can anyone tell me how to extract the base quality from the CQ field of the BAM file? I colleague of mine mentioned that every two ASCII character corresponds to the SOLiD color space. Do I take the average of every overlapping 2 or the max? Any input in this regard is gretaly appreciated!
Is the base quality not already reported in the SAM record (it should be)? As to how to calculate the base qualities during alignment from color qualities, here is the formula MAQ/BWA/BFAST uses:
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