Ion Torrent data with RC454

[Armand Bester]

I am interested in using the Broad pipeline for HIV deep sequencing with Ion Torrent.  I was wondering if it would be valid to use rc454 on Ion Torrent data for indel correction after assembly with vicuna and then use vphaser/vprofiler to do the variant calling.  Any advice would be much appreciated.

[Michael C. Zody]

We haven't tested the pipeline on IT data, but we believe that the protocols for 454 data analysis should work directly on IT. We expect that there will be fewer CAFIE errors to be corrected, but the error modes should be the same when they do occur.

Mike