The Mutation Annotation Format (MAF) is used by the TCGA project to annotate somatic mutations (e.g. missense or frameshift mutations) in different types of cancer. In order to visualize these data, we use maftools. maftools provides both summarizing statistics and various plots to get an overview of the data. In this tutorial you will learn how to access MAF files from the Pancreatic Adenocarcinoma, add them to a project on the Cancer Genomics Cloud (CGC for short), run maftools and visualize some results.
- Select MAF files from the Pancreatic Adenocarcinoma
- Import the files into your project
- Use maftools to visualize the MAF file
The CGC platform allows you to query the TGCA dataset in an easy and visual way. This short video illustrates how to select a subset of cases based on a combination of different critera. Here we select case files
- with a diagnosis of Pancreatic Adenocarcinoma (
Disease type) - that are open access (
Access level) - in the MAF format (
Data format)
This is the search interface for all the TCGA data available on the CGC platform.
Here, please select the red Case category.
After selecting the Case category, please click on the purple File category to add properties to the query. In a first step, please select the Disease type category and search for Pancreatic Adenocarcinoma
Tick the Pancreatic Adenoncarcinoma box and click the Add property button.
Please select the Access level property and then select open
Please select the Data format property and then select MAF
This is the finished query:
After selecting files, we add the files to our project called maf_exploration.
In order to add the files to our project, please click the green + Copy files to project button in the upper right corner. Then select your project by name.
Files are listed in the Files tab in the maf_exploration project
In this step, you will run maftools to produce some summary statistics and plots for the input MAF files.
To import the CWL on your project, Go on the Apps and click on + Add app. Then click the green Create Tool button, enter the name "maftools" in the dialog and click create.
Then select the button right next to run shown three dots on the top right. A menu opens and click on Import Json, and import from URL: https://raw.githubusercontent.com/sbg/maftools/cwl-desciption/maftools.cwl.json
After importing maftools using the instructions above, you can now select one of the input files you added to the project and run maftools.
First, you select Apps from the tabs menu, then select maftools. This page presents an overview of the tools, usually contains some documentation and describes which input files and parameters are needed. Next, please click the green Run button on the top right. In the Set input data tab, please select one of the MAF files you added to the project. Now, click Run again and confirm your action. This submits the task and we now can relax, lean back and wait until our task has finished.
This small video illustrates the process:
After the application is launched, you can expect two main outputs:
A description of all plots is available on the maftools homepage in the visualization section.