Home

Welcome to the diagnostics_exome_reporting wiki!

This project initially started as a means to provide automated, unified and comprehensive variant annotation routines to the diagnostic team in our laboratory. It has since morphed into something which at it's base level still revolves around this but has become much more flexible and feature rich. While the name of the repository includes exomes this pipeline is able to run on variant data provided in a standard VCF file format.

What does it do?

This tool provides a user friendly Graphical User Interface (GUI) to a series of custom scripts which perform extensive variant annotation and filtering based on a series of provided gene lists (tiers). The final output includes a detailed report (generated via RMarkdown), an annotated VCF file, 'friendly' formatted csv files for each tier of variants and a log file reporting on the run.

A manuscript documenting the methods and development of our pipeline is currently in production: draft at Authorea

Variant annotation, filtering and reporting tool

This repository

Shiny framework for visualisation and interactive filtering

A separate module that was developed alongside the variant annotation tool, this is available via it's own GitHub repository.