Case Study: Building Analysis Workflows for Linkage Studies in the Syllego System

Geneticists, biologists, and statisticians have several analysis programs to choose from when analyzing genotyping data. Some of these programs may be proprietary while others are open-source and available online; however, these programs may only exist as command-line applications. For researchers without computer programming experience, using these programs to execute an analysis can be challenging.

The Rosetta Syllego™ system provides a user-friendly interface to work with almost any external analysis program—open source or proprietary. These external analysis programs are integrated into the Syllego system as analysis workflows. The Syllego system version 2.0 provides pre-configured analysis workflows for association analyses; however, you can also build additional workflows for the analysis method of your choice.

This brief case study describes how to build analysis workflows by importing workflow files.

Download, Import, and Build Additional Analysis Workflows

Analysis workflows allow you to format your data from the Syllego system, execute the analysis and then import and view analysis results back to your Syllego system client. In the Syllego system 2.0, analysis workflows for PLINK^[1][2], the open-source genome-wide association toolset, are pre-configured and available for you to use immediately.

However, we recognize that customers may need additional programs. For example, customers who want to conduct a linkage analysis using the open source program, MERLIN^[3][4], will be able to download the analysis workflow file for MERLIN from our Support Web site^[5] in the future.

Installing the MERLIN Analysis Workflow

The following paragraphs describe how to download the MERLIN workflow once it becomes available, and how to import it into the Syllego system.

Visit the Rosetta Biosoftware Support Web site. Log in or register for an account to view the Downloads page under Syllego system support materials. Under Downloads, visit Analysis Workflows page and search for the analysis workflow you need. Typically, available analysis workflows for download from this page—including MERLIN, Allegro, and Haploview—are packaged as "workflow" files. These workflow files contain file templates and programs to allow the Syllego system to properly interface with external analysis programs. Click on the MERLIN file to download and save it to your local hard drive.

Next, the MERLIN workflow must be imported into the Syllego system. Open the Syllego system client on your workstation. Select Analysis Workflows in the Navigator, and then go to the Data section under the Home tab and select Import. Browse and select the MERLIN workflow file previously downloaded, and click OK. (Figure 1).

Figure 1: Importing a MERLIN workflow file.

To run the MERLIN analysis, select your data source (genotype data, individual list or SNP list) in the Navigator, and select Linkage Analysis from the Run Analysis section under the Analysis tab. A dialog window will open with available linkage study workflows to choose from; select MERLIN from the linkage analysis menu. The Syllego system will then run the workflow as a series of steps to get results.

All the file templates and analysis program used in this run the MERLIN workflow were imported at the same time with MERLIN workflow file. The analysis programs make up steps in the analysis workflow. Analysis programs sometimes need templates for data conversion and configuration tasks. To view each step in a workflow, double click on the MERLIN workflow in the Navigator (Figure 2).

Figure 2: View components of the workflows, and the steps for running the workflow.

As pictured in Figure 2, your data source is first selected and configured. Upon the data source selection, a file template will convert your data into analysis-ready files for MERLIN. The third component runs an executable analysis program, aka MERLIN. Finally, the last component imports results from MERLIN and creates analysis results in the Syllego system.

At this point, the imported MERLIN workflow is not published, meaning that the workflow cannot be used by others. To publish this workflow, select MERLIN in the Navigator, and go to select Publish in the Publish section under the Home tab.

Use the Analysis Method of Your Choice

The Syllego system provides several options for using analysis workflows of your choice: you can use pre-configured workflows for the association analysis toolset, PLINK, or download and import workflows as they become available from our Web site.

In addition, you can build custom analysis workflows with a Analysis Workflow wizard in the Create New section of the Home tab. This wizard takes you step-by-step through the process of building your workflow, allowing you leverage third-party applications, such as R.

For more information, visit the Syllego system Web page.

Back to Messenger, Volume1, Issue 2

[1] Shaun Purcell, http://pngu.mgh.harvard.edu/purcell/plink/
[2] Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ & Sham PC (2007) PLINK: a toolset for whole-genome association and population based linkage analysis. American Journal of Human Genetics, 81.
[3] http://www.sph.umich.edu/csg/abecasis/MERLIN/index.html
[4] Abecasis GR, Cherny SS, Cookson WO and Cardon LR (2002). Merlin-rapid analysis of dense genetic maps using sparse gene flow trees. Nature Genetics,  30:97-101.
[5] http://www.rosettabio.com/support/syllego