Structural variations using Newbler mapper

[Soni]

Hi,

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?

Cheers

Soni

[vamosia]

Have you checked the 454AllStructVars.txt? One possibility is that there wasn't enough confidence in that that particular "deleted" region to classify it as "High Confidence".

Such variations would in turn be categorized in the 454AllStructVars.txt, which uses a lower threshold.

[Soni]

Thanks for your reply vamosia. That is exactly why it is baffling me as those SVs have 'High' confidence and are in the 454HCStructVars.txt.