• Manuals

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• Introduction
• Ingenuity Variant Analysis
• Ingenuity Variant Analysis for Hereditary Diseases
  • Genetic disease pipelines
  • Pipeline description and supported input
• Workflows
  • Identify and Interpret Causal Variants in a Trio using IVA (WGS)
  • Identify and Interpret Causal Variants in a Trio using IVA (WES)
  • Identify Somatic Variants from a Single cfDNA Sample using IVA (WES)
• Analysis using the plugin and the IVA web interface
• Add Information from Allele Frequency Community
• Remove Variants Found in Allele Frequency Community
• Changing Allele Frequency Community opt-in settings
• Install and uninstall plugins
  • Install
  • Uninstall

Introduction

Ingenuity Variant Analysis plugin provides the ability to carry out an Ingenuity Variant Analysis on variant tracks generated in the Workbench, and to annotate and filter variants based on information present in the Allele Frequency Community. The latest available content from the Ingenuity Knowledge Base and Allele Frequency Community is used in the biological interpretation of input variants from whole genome, whole exome, targeted amplicon, or whole transcriptome sequencing experiments. By using published biological knowledge of disease biology, the Ingenuity Variant Analysis plugin can be used to prioritize your variants. The purpose of the integration is to supplement the abilities of the Workbench with the biological knowledge available in Ingenuity Variant Analysis and the Allele Frequency Community.

The plugin bundles four tools, which can be found in the Ingenuity Variant Analysis folder in the Toolbox:

• Ingenuity Variant Analysis, used to analyze cancer genomes or to carry out stratification analysis
• Ingenuity Variant Analysis for Hereditary Diseases, used to analyze genetic diseases
• Add Information from Allele Frequency Community, used to annotate with information from the Allele Frequency Community database
• Remove Variants found in Allele Frequency Community, used to filter out variants that are present in the Allele Frequency Community database

In addition to the four tools, the plugin comes with three ready-to-use workflows installed under the respective applications in the toolbox (Whole Genome Sequencing or Whole Exome Sequencing).

• Identify and Interpret Causal Variants in a Trio using IVA (WGS)
• Identify and Interpret Causal Variants in a Trio using IVA (WES)
• Identify Somatic Variants from a Single cfDNA Sample using IVA (WES)

Furthermore, the plugin includes the possibility to update a variant track containing the results of an Ingenuity Variant Analysis, if you change the filtering settings inside the Ingenuity Variant Analysis web interface.

Access to Ingenuity Variant Analysis requires a subscription. However a one-month trial period is available and allows the analysis of up to 4 samples. The first step is to register for an Ingenuity Variant Analysis account https://apps.ingenuity.com/isa/account/signup/va?utm_source=ingenuity&utm_medium=banner&utm_campaign=webpage-preview. Upon completion of registration, you will receive an email to activate your new Ingenuity Variant Analysis account. Once you've logged in for the first time and accepted the End User License Agreement, you can use these credentials to allow the plugin to send variant data from CLC Genomics Workbench to Ingenuity Variant Analysis.

If you opt into the Allele Frequency Community, you will get a month of free analysis without a subscription to Ingenuity Variant Analysis. See Changing Allele Frequency Community opt-in settings to change your Allele Frequency Community opt-in status.

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