Bulk data and using the tool library

This article explains the UK Biobank Research Analysis Platform (UKB-RAP) tool library, a collection of commonly used apps and workflows, and how to use them to run your analysis using the app "Swiss Army Knife" as an example. This tutorial is part of the overview series introducing researchers to the data and functionality of the UKB-RAP.

Navigating the tool library

You can navigate to the tools library via the tools tab.

Some software in the tools library such as Swiss Army Knife can be used to work with bulk UKB data. Other apps like table exporter can be used to work with and extract phenotypic data.

Example: Swiss Army Knife

Swiss Army Knife contains a collection of many handy genomics tools (hence the name), including samtools, vcftools and many more. For an overview of these tools, please see this tools library page.

To run this tool:

• Navigate to the tools library
• Select Swiss Army Knife
• Click the “Run” 

This will open a pop-up window where you must specify the output directory for your results.

• Select "Next"

This will take you to the tools execution page.

Inputs tab: Specify various input parameters, with required input parameters highlighted in orange.

Outputs tab: Location where results will be written.

Instance tab (top right corner): Specify configurations for the instance the job will be run on. For more on instance types, see this page. For information on the costs of these instances, please see the UKB-RAP rate card.

Documentation tab (top right corner, beside the instance tab): Click to see documentation about the tool.

Example: using vcftools to calculate the allele frequency for a given file

As previously mentioned, there are many tools within Swiss Army Knife- for this example, we will be using vcftools to calculate the allele frequency for a given file.

Specify inputs:

• Input file: select your chosen VCF file.
• Command line: Specify the tool you wish to use by typing in a command. A list of Swiss Army Knife commands can be found in the tools library. For example, to specify for vcftools:

vcftools --gzvcf *.vcf.gz --freq --out freq_analysis

Then, you can click start analysis to run the job. You will need to specify the priority of the job before launching the analysis. Make sure to check the progress of the job via the monitor tab.

Alternative Way: Using dx fuse

It is not necessary to specify an input parameter when using dx fuse. dx fuse is a file system that allows users to access storage in the DNAnexus system. It is only available in certain apps.

Instead of specifying the input parameter, instead you can put the file path directly in the command line prompt. For example:

vcftools --gzycf “/mnt/project/demo_material/example_vcf.g.vcf.gz” --freq --out freq_analysis

Click “Start Analysis” and launch the job, and make sure to check the progress of the job via the monitor tab.