gap penalty in BWA

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Victory

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Join Date: Nov 2009

Posts: 13
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#1

gap penalty in BWA

11-13-2009, 12:40 PM

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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annguyen

Junior Member

Join Date: Nov 2020

Posts: 4
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#2

01-14-2021, 07:19 AM

I think those are default penalty weights:

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