IGV Session Generation

Implementation of the igv_session_generation step

This step takes as the input the output of the following steps and generates an IGV session XML file that displays the results as genome tracks:

ngs_mapping
variant_annotation or variant_calling

Step Input

The IGV session generation step takes as the input of the following CUBI pipeline steps:

ngs_mapping
variant_annotation or variant_calling

Step Output

Global Configuration

Default Configuration

The default configuration is as follows.

# Default configuration igv_session_generation
step_config:
  igv_session_generation:
    path_ngs_mapping: ../ngs_mapping
    # One of the following must be given!
    path_variant_phasing: ''
    path_variant_annotation: ''
    path_variant_calling: ''
    tools_ngs_mapping: [] # defaults to ngs_mapping tool
    tools_variant_calling: [] # defaults to variant_annotation tool

Reports

Currently, no reports are generated.