Mismatch setting for bwa mem ?
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4.7 years ago
Picasa ▴ 610

Hi,

Can we set the mismatch number for bwa mem ? And by the way what is the default number ?

Thanks

bwa mem mismatch • 4.8k views
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According to bwa manual

-B INT  Mismatch penalty. The sequence error rate is approximately: {.75 * exp[-log(4) * B/A]}. [4]
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This is the mismatch penalty for the score but it does not say how many mismatchs are allowed

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Discussed before (see right panel). TL;DR There is no such parameter, you can screen the resulting bam file.

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