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Old 01-11-2012, 10:03 AM   #1
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Default BWA:getting hits with given number of mismatches and indels

is it possible to setup BWA to get hits with at most x mismatches and y indels? Although -n x -o 1 -e y would allow x mismatches and y consecutive indels, what if I want to permit non consecutive indels to be reported?
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