How to analyse tumor data and publish the results

Background

You need to process tumor sequencing data to extract key genomic alterations. Cancer genomics portals help you explore and share these results, but they require data in a specific structured format.

Scenario Overview

You start with raw tumor sequencing files, run an analysis workflow to generate variants and copy number profiles, then format the outputs so they can be uploaded to a cancer genomics portal for exploration.

Complexity

High

Environment

HPC or Cloud

Outcome

Published dataset

Prerequisites

Before starting this scenario, you should have the following prerequisites in place.

Set up HPC environment

Collect and stage tumor sequencing data

Your Journey

Run the tumor analysis

Prepare the portal-ready dataset

Convert pipeline outputs to portal-compatible formats.

Take the standard outputs from oncoanalyser (VCF, copy number tables, fusion calls, expression files) and convert them into the simple tabular formats and study metadata structure required by cancer genomics portals. This step connects the pipeline results to the portal by mapping each output type to its corresponding portal file.

Examples

Bioinformatician

I have the oncoanalyser VCF and copy number outputs and need to reformat them into the specific MAF and SEG files that cBioPortal expects for data import.

Data Manager

I need to ensure the clinical annotations and sample metadata are properly structured to match the portal's data model before uploading.

Tools and resources

oncoanalyser outputs Documentation

cBioPortal file formats Documentation