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Old 06-06-2017, 01:52 PM   #232
jweger1988
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Location: Paris, France

Join Date: Apr 2017
Posts: 37
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Brian,

Thanks for the quick response.

It seems like splitting it up does give me a little better precision (as judged by a higher % of bases lost), so I'll stick with that.

On a similar note, I'm wondering what your thoughts are on quality trimming. If I trim to q30 (qtrim=rl trimq=30) I lose about half my bases. Do you think this level of stringency is required for variant calling? What would you normally do?
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