README.md

sv-path-predictor

A Snakemake pipeline to predict structural variant pathogenicity and outputs a compound score calculated from three different predictors. It uses CADD-SV, TADA, and StrVCTVRE.

Pipeline overview

Getting started

1. Install Snakemake version >= 6.7.0
2. Clone the repo and cd sv-path-predictor/
3. Prepare the inputs: config/manifest.tab and config/config.yaml
   1. cadd-sv specific- you must have these softlinked to the directory
      1. ln -s /path/to/softwares/pipelines/CADD-SV/annotations/ .
      2. ln -s /path/to/softwares/pipelines/CADD-SV/models/ .
4. If the dry run -np looks good, start your analysis

   snakemake -s sv_path.smk --printshellcmds --use-envmodules --use-conda

Requests/TO-DO

• Kumara suggests we allow bed file as input to filter the input VCF.
• Add https://github.com/lgmgeo/AnnotSV