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Old 12-05-2012, 10:34 PM   #6
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Location: San Diego, CA, USA

Join Date: Sep 2009
Posts: 438

Originally Posted by adaptivegenome View Post
Mapping quality is valuable for variant calling. If the quality score does not correspond to accuracy of alignment, this is a big problem I think.
You're right about that. That's probably why it's better to use BWA for those alignments. I don't know of any advantage other than speed for using bowtie2 over BWA. I haven't done any hardcore comparisons between the two. I do like BWA's alignments more though...not sure why.
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