scvep

Super Cereal VEP

Annotation-free variant effect prediction for, well, unannotated reference genomes/transcriptomes.

Requires ktio library: pip install ktio (--target /path/to/scvep IFF no root/superuser access/own python environment on system) and a local blast+ installation, i.e. blastx in path

Installation

1. git clone https://github.com/krasileva-group/scvep.git
2. cd scvep
3. pip install -e .

Usage

1. Build reference database for target organism/family etc., according to the example in prepare_db.sh
2. Run with python scvep.py (or after installation with pip with scvep) <snps.vcf> <scaffolds.fasta> </path/to/reference_db>. scvep will generate two tables, a) unfiltered blast output and b) predictions on filtered blast hits.