I would like to run your new SVFX method on some structural variants. For full disclosure, I’m working on a method to assess the pathogenicity of germline SVs, and would like to compare with yours. Based on reading your preprint, I believe our methods are quite distinct in terms of training data. I think it’s great you’ve already put code on github, but I’m not sure what data files are needed to run the code. Could you put me in touch with one of your students to help me run SVFX locally?
Thanks for your interest in SVFX. We have reported our feature list in supplement table1.
Overall, our feature list is extracted from a bunch of genomic annotations and various functional genomics/epigenomics signal files.
You can download signal files from iHEC or epigenome roadmap data portal. As you might have noticed, we created multiple tissue-specific models for our analysis.
For the germline model, we also built a feature matrix based on the h1HESC cell line, which performed quite well. On the SVFX GitHub page, we have uploaded the bed file for different annotations (under the data folder) used in our study.