Instructions for Query (Web UI)
The following document walks through the steps for running a query against the CHORUS database through the DNAnexus web user interface (web UI).
CHORUS queries are powered by DNAnexus. You need to have a DNAnexus account in order to perform queries.
If you have not agreed to the terms of use, please contact Pauline Ng ([email protected]) and Jack Ow ([email protected]) to agree to the policy of use for CHORUS queries, and an account will be created for you.
CHORUS requires input files conformant to the VCF specification. VCF files are the typical output of most variant callers (such as GATK, FreeBayes, and ISAAC) and other secondary analysis tools.
You can upload files through the DNAnexus web UI, more information can be found on the DNAnexus wiki.
The CHORUS Query app is open to selected users during the current beta-testing phase.
To check whether you have access to the CHORUS Query app, log in to your DNAnexus account through our login page; navigate to any project or create a new project.
Once you're situated in a project, click the green Start Analysis button (red box below).
A pop-up list of available tools will appear. Type "CHORUS Query" (or a substring of it) in the search box (red box) to check that "CHORUS Query" is found within the list of apps you have access to.
If you don't see an app of this name, you may not have access to this app at the moment. To request access, please contact Jack Ow ([email protected]) and Samantha Zarate ([email protected]).
Like before, log in to your DNAnexus account and navigate to a project where your input VCFs are stored.
Click the green Start Analysis button, a pop-up list of available tools will appear. Select the "CHORUS Query" app by clicking on it.
If this is the first time you're running the "CHORUS" app, you will be prompted to agree to "installing" this app. Click on the green "Agree and Install" to install this app. You will only need to perform this step once.
A "Run Analysis" dialogue will appear. In this dialogue, a row represents an executable tool, whereby input files are listed on the left and output files are listed on the right.
Click on the "input VCF" box to select the input VCF file that you want to issue the CHORUS query against. You can browse the current project you're in or select a file found in another project you have access to.
Click on the "gear" icon to view additional options and parameters of the CHORUS Query app (red box below).
In the pop-up configuration page, of special interest is the option build, which specifies the reference genome build used to produce the input VCF. Currently, hg19 and hg38 are available build options, and these 2 builds are supported by all cohorts in CHORUS. (Note that hg19 is also known as GrCh37 and hg38 is also known as GrCh38; the query app will automatically handle the addition/removal of chr from chromosome names).
Click Workflow Action > Set Output Folder to redirect the output file to a specific folder in the project.
Click on Run as Analysis to launch the query.
You can monitor the progress of the query in the Monitor tab of the project.
In the monitored job page, you can quickly navigate to the input and output files using links provided in the bottom half of the page.
- Input file format: Ensure that your input file conforms to the VCF specification, including properly formatted header lines.