Consequence prediction pipelines for ClinVar/Open Targets

This repository contains two modules and their corresponding wrapper scripts:

• vep_mapping_pipeline: maps variants (CHROM:POS:REF:ALT) to their most severe functional consequence according to Ensembl VEP, as well as their Ensembl gene ID and name.
• repeat_expansion_variants: parses ClinVar variant_summary file and extracts information about repeat expansion variants.

Please see the corresponding module README file for more information.

Installing requirements

The commands below has been tested for Ubuntu 19.10. You might have to adjust commands and package names if you're using a different distribution. Note in particular that some older Debian and Ubuntu distrubutions include ancient htslib/ samtools/bcftools versions.

sudo apt -y install samtools bcftools parallel libbz2-dev liblzma-dev
sudo pip3 -q install -r requirements.txt