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Old 11-19-2010, 12:18 PM   #4
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Join Date: Jan 2008
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Originally Posted by nilshomer View Post
BWA does not consider quality scores so you need to convert the quality scores in the SAM/BAM file to sanger before variant calling.
thats a shift from MAQ which does use base Q values to do alignments. Wouldn't BWA achieve greater efficiency in using base quality values of mis-matches to weigh them and penalize accordingly!
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