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Old 12-09-2016, 02:57 PM   #11
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
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Quote:
Originally Posted by antoinefelden View Post
I'm re-running the whole job with samtools 0.1.19, I'll post the outcome here.
You don't need to rerun the whole job... the only problematic part is sorting and indexing the mapped reads. If you use samtools 0.x, it will work fine using the existing output of BBMap. But you can also use samtools 1.x if you look into the manual and find whatever arcane invocation is appropriate now. Hopefully there is a command that will work with all versions of samtools; I'll adjust the "bs" output in the next release.

Last edited by Brian Bushnell; 12-09-2016 at 11:23 PM.
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