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Old 11-13-2009, 11:40 AM   #1
Victory
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Location: Pennsylvania

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Default gap penalty in BWA

Hi,
I have short question about gap penalty in BWA. The manual said that the gap open penalty is 11 and gap extension penalty is 4. Does the first gap position will be charged 11 or 15?
Thank you
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Old 01-14-2021, 06:19 AM   #2
annguyen
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I think those are default penalty weights:

Gap open: cost to make gaps
Gap extension: cost to make gaps bigger
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