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Old 06-13-2010, 04:20 PM   #4
Location: Japan

Join Date: Feb 2009
Posts: 10

Hi Torst,
Thank you for your reply. I agree with you. Quality scores of deletions is informative. But if the pileup format (made by BWA->SAMtools) was designed based on the IDEA you said, inserted bases should have base quality scores. Actually, however, inserted bases don't have qualities as below. I'm confusing...

chr3 7759 C 4 ..,, SO]^
chr3 7760 C 4 .+1G.,, \\\[ <-- 4 ref-type bases and 1 insertion, but only 4 qualities
chr3 7761 G 4 ..,, GT[a
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