Ingenuity Variant Analysis
To start the tool, go to Ingenuity Variant Analysis | Ingenuity Variant Analysis
If you are connected to a server, you will first be asked about where you would like to run the analysis. If you are not connected to a server, the first step is to specify the input for the analysis. The Ingenuity Variant Analysis tool accepts variant tracks () as input. Select the desired variant track or several variant tracks as input, as shown in figure 2.1. All the variant tracks selected in this step are assumed to be "case" samples.
Figure 2.1: Select the variant track that you would like to analyze.
In the following dialog, you can set the Variant analysis parameters (figure 2.2).
Figure 2.2: Specify analysis parameters.
- Reference: Select the human reference sequence that is found
under CLC_References in the Navigation Area. Complete human genomes (e.g., hg19 (GRCh37) and hg38 (GRCh38)) and subsets of these (e.g. individual
chromosomes) can be used as references.
- Control tracks: This is an optional parameter. You may select one or more variant tracks, which will be considered to be "control" samples in the analysis.
- Analysis pipeline name: Select the pipeline appropriate for your analysis. The Ingenuity Variant Analysis is performed with predefined settings that differ depending on your choice of analysis pipeline. The following options are available:
- Cancer: Useful if you are seeking to identify cancer driver variants. If this option is selected, the type of cancer must be specified in the Disease name drop-down menu.
- Stratification study: Useful if you have two groups of samples and are looking for variants that distinguish the two.
- Variant Analysis Custom Pipeline: Useful if you have already carried out an Ingenuity Variant Analysis, where you have set up a desired filtering cascade, and want to re-use the same filtering cascade for a new analysis. If this option is selected, the name of the custom analysis must be specified in the Custom analysis name field. The name you enter in the Custom analysis name field must match the "Name" field of an existing analysis in Ingenuity Variant Analysis, exactly as it appears in the Ingenuity Variant Analysis web interface. Note: please provide unique names to all your custom analyses in Ingenuity Variant Analysis: you might not be able to reuse a filtering cascade if its name was already used previously, even in cases where that previous analysis was already deleted.
- Upload only: Useful if you just want to upload samples and do not wish to carry out an analysis. Note: in this case, no results will be downloaded.
- Analysis name: The name of the analysis. You can enter a name of your own choice by typing in the name, or by using the options that appear when you press Shift + F1. The available shorthand notations are: {input} will be substituted with the name of the input experiment, {date} is substituted with a date stamp, and {pipeline} is substituted by the Analysis pipeline name. The analysis name is the name that is shown on the Ingenuity Variant Analysis page when you choose "My Analyses". The same analysis name can furthermore be used in a Variant Analysis Custom Pipeline, if you specify it in the Custom analysis name field (see above).
- Analysis description: This will be the description of the analysis in Ingenuity Variant Analysis once created. There are a few shorthand notations available: {input} will be substituted with the name of the input experiment, {date} is substituted with a date stamp.
In the "Account information" dialog, enter your Ingenuity username (email address) and password (figure 2.3). If you do not have an Ingenuity username or password, you must first create an Ingenuity account (see how in the Introduction).
Figure 2.3: Specify the account information: your Ingenuity username (email address) and password are required.
The "Result handling" dialog allows you to set the output options (figure 2.4).
Figure 2.4: The result handling step in the Ingenuity Variant Analysis wizard.
If the Import annotated and filtered variants option is checked, the tool will produce a variant track as output. If it is unchecked, the analysis will be created, and can be accessed inside the Ingenuity Variant Analysis web interface, but the results will not be imported into the workbench. Note: it is not possible to import results if you have selected the Upload only pipeline earlier in the wizard.
If you choose to Open the results the two generated outputs will be opened in the View Area without being saved. In this case you will have to manually save the outputs if you would like to keep them. If you choose to Save the outputs, click Next to specify where to save the results. Click Finish to start the Ingenuity Variant Analysis. Your results will not be opened automatically but will be saved at the destination you have specified.
The outputs and how to manually adjust filter settings are described in Analysis using the plugin and the IVA web interface.