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Old 03-29-2011, 04:34 AM   #1
gurkly
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Default how to get all hits of equal quality?

Dear all,

using bwa, how can i get all alignments/hits of equal best quality reported?

Also, how can one get the additional sam output fields (such as alignment score, AS etc.) from bwa.

Many thanks in advance!

G.L.
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Old 03-29-2011, 08:56 AM   #2
gurkly
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Could anyone please help?
(I'm not finding this info on the bwa manual pages)
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