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Old 12-06-2011, 04:08 AM   #1
Location: Nairobi

Join Date: Oct 2009
Posts: 11
Default Structural variations using Newbler mapper


Would anyone know how gsMapper decides on a consensus especially over a region that has structural variations? I am looking in 454HCStructVars.txt and 454HCStructRearrangements.txt to identify large structural variations (SV). When I look at the assembly over the region with the variation (e.g. deletion) the deletion is not reflected in it, as in there is sequence spanning the “deleted” region. The variation frequency for these SVs is also high (around 70%).

Would you know what’s going on or what’s the best way to interpret the SV output from gsMapper?


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