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Old 08-19-2014, 12:37 AM   #4
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

It can be a pain to tweak bowtie2's local alignment setting to get decent results (that's one of the reasons I have Bison default to end-to-end alignment). BWA-meth's defaults are pretty reasonable and might give decent enough results, though as frozenlyse mentioned, ion torrent data is often riddled with InDels. Brent's pretty good with timely feedback, so you might just drop him an email if you don't get decent results.

BTW, you can also try sending me a small test dataset and I can have a look with Bison and see if I can send you some reasonable settings, though I expect BWA-meth will work.
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