Readme
Introduction
A quick Ruffus script for annotating vcfs with VEP.
There are a few preprocessing steps required before annotation so decided to do as a pipeline.
Really just so I can learn a a bit of Ruffus syntax.
Running
python vep_annotate_pipeline.py --input_dir vcfs/ --config_file config.txt --vcf_header_file header_file.txt
Options
- --input_dir = The folders with the vcfs in (.gz expected)
- --config_file = The file with the configuration information in e.g. location of folders, reference genom etc
- --vcf_header_file = The file with the vcf headers to add