PEDIA-workflow usage and program documentation

This application implements a workflow for exome variant prediction of human genetics cases on the basis of variant, feature and photographic gestalt information. In order to extend the available data, a large number of cases without exome sequencing results are used for simulation of exome simulation to train and test the PEDIA classifier.

Gene predictions are sourced from Face2Gene and Phenomizer by translating predicted Syndromes to genes. Detected pathogenic variants are cleaned using Mutalyzer and converted to VCF with Jannovar.

This document contains instructions for general installation and usage of the pipeline, but also deeper implementation details for those interested in understanding and changing the source code.

Contents:

• Installation instructions
• General usage
  • General structure
  • Downloading
  • JSON Parsing
  • Phenomization
  • VCF Generation
  • Quality Check functions
  • Error correction overrides
• Implementation details
  • API Components structure
  • jSON Parsing and Case generation
  • Configuration and external usage interface

Indices and tables

• Index
• Module Index
• Search Page