Hi everyone, I am planning to run only the structural variant (SV) analysis on whole genome sequencing (WGS) data for a single sample. I already have the gnomAD-SV BED file, the appropriate genome reference, and the VEP cache (113_GRCh38) prepared. I would like to ask what additional inputs are necessary to properly evaluate and rank the SVs using these resources. In particular, I’m a bit unsure about the parameters

score_config_sv

and

svdb_query_dbs

in the configuration file. Could you please clarify their roles and whether they are essential for this type of analysis? Thank you in advance.

Hi Harsh!

score_config_sv

is used to supply a configuration file for genmod to rank structural variants.

svdb_query_dbs (or svdb_query_bedpedbs)

is used to supply annotation databases to svdb. Yes, these parameters are mandatory if you want to annotate and rank your variants.

Hi @Ram, Thank you for your kind response. As I review the GitHub documentation, I see that several pre-rocessing scripts are required to clean the downloaded VCFs especially for `gnomad_SVs`—I’m currently working on that step. I had one major question regarding `Genmod`: does its variant/mutation ranking system offer prioritization comparable to tools like

Exomiser

or other state-of-the-art methods?