Annotate Structural variants with population specific allele frequency values
Has anyone tried filtering structural variants based on pupulation specific allele frequency (AF) values (for example gnomAD-SV or phase 3 1000 genome SV)?
I have a set of SVs that I detected using a multipronged approach. For prioritising variants, I wanted to remove SVs that are common variants in my population of interest (AF>0.05). In order to get population specific AFs for my detected SVs, I came across gnomAD-SV here: www.ncbi.nlm.nih.gov/dbvar/studies/nstd166/
Am I missing something here that I am not getting any variant overlap between the query and target VCFs? The genome versions used seem to be the same. Anyone who has successfully done the above work, or tried doing it, can they please let me know if I am doing it right, or I have to pre-process the dbVar VCFs in any way?