TSOPPI: TSO500 Post-Processing for InPreD

‘TSOPPI’ is a collection of tools for post-processing of data generated by Illumina’s TSO500 LocalApp pipeline. Packaged in a Docker/Singularity container, the aim of the software is to annotate, integrate and visualize the somatic variant calling results produced by the primary LocalApp analysis.

Please refer to the documentation pages of individual tools for details regarding their functionality and usage.

Table of contents:

• Getting started
  • Prerequisites
  • Individual TSOPPI tools in the data analysis workflow
  • TSO500 LocalApp
  • TSOPPI Docker image
  • TSOPPI Singularity image
  • Contact
• Metrics plotting tool
  • About
  • Metric types
  • Input files
  • Additional notes
  • Running the tool
  • Output files
• Variant summary creation tool
  • About
  • Input files
  • Running the tool
  • Output files
• Variant recurrence table creation tool
  • About
  • Input files
  • Running the tool
  • Output files
• Sample data post-processing tool
  • About
  • Functionality overview
  • Running the tool
• Sample comparison tool
  • About
  • Functionality overview
  • Input files
  • Output files
  • Additional notes
  • Running the tool
• ICNVA tool
  • About
  • Functionality overview
  • Input files
  • Output files
  • Additional notes
  • Running the tool
• SAmple Data Extraction Tool
  • About
  • Functionality overview
  • Input files
  • Output files
  • Additional notes
  • Running the tool
• InPreD sample ID nomenclature
• Software versions
• Frequently asked questions
• Change log

Indices and tables

• Search Page

(last updated: 2024-12-05)