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Old 12-09-2016, 02:38 PM   #10
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

OK! I've tested this with samtools 0.1.19 and 1.3.1, and it fails with samtools 1.3.1. Apparently this is caused by some basic parameters that were changed when samtools migrated from 0.x to 1.x; this is something that I advocate against, but it it is sometimes unavoidable. Sorry about that! I'll release a new version soon that will work with both samtools 0.x and samtools 1.x, if that's possible. In the meantime, of course, you can use samtools manually...
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