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.

step_config:
  igv_session_generation:
    #path_ngs_mapping: ../ngs_mapping
    #path_variant_phasing: ''
    #path_variant_annotation: ''
    #path_variant_calling: ''
    #
    # defaults to ngs_mapping tool
    #tools_ngs_mapping: []
    #
    # defaults to variant_annotation tool
    #tools_variant_calling: []

Reports

Currently, no reports are generated.