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mrfox

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Join Date: Aug 2010

Posts: 103
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BWA parameters

07-25-2012, 08:49 AM

Hi guys,

I am going to use BWA and GATK to detect SNPs and small indels in one of my projects. This is my first time to use BWA. I would like to know what are the parameters you guys use for BWA? Which parameter is associated with uniquely mapped/best quality reads?

Thank you very much.
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