Filtering based on iAnnotateSV results

[anoronh4]

Thanks for this really nice tool! I was wondering if there are any recommendations for filtering tumor variants after they are annotated. It has been suggested by a colleague to filter any variants where DGv_Name-DGv_VarType-site1 and DGv_Name-DGv_VarType-site2 match exactly, but I have seen places where the one is only a partial string match of the other, and i'm not sure what to do in the case of more complex annotations, for example:

DGv_Name-DGv_VarType-site1	DGv_Name-DGv_VarType-site2
nsv870829-Gain<=>nsv7177-Inversion<=>nsv829649-Loss	nsv7177-Inversion<=>nsv829649-Loss

The string nsv7177-Inversion<=>nsv829649-Loss is in both, but the first column contains: nsv870829-Gain<=> in addition. I'm not sure how to interpret the values when they contain <=>.

If there's any other way we could filter using the annotations from this tool, we would definitely love to know!