Genetic disease pipelines
The following pipelines can be used to identify variants associated with genetic disease. Each pipeline will run an analysis and specifically return variants with the indicated mode of inheritance.
- Dominant inheritance pattern
- This disease is caused by a de novo mutation.
- This disease is caused by a recessive compound heterozygous variant.
- This disease is caused by a recessive homozygous variant.
Note that the genetic disease pipelines listed above correspond to the analyses that can be run from the Ingenuity Variant Analysis web interface, with the exception that the constituent filters are static when running them from the workbench (running them from the IVA web interface means that filters that do not let any variants pass through are automatically removed).
The user is encouraged to review and customize the best practice filter cascade settings as they see fit through the IVA web interface after the workbench analysis has completed. The filter cascade that corresponds to an analysis can be easily found by right-clicking the open analysis result variant track, and selecting "Launch Ingenuity Variant Analysis (in browser)". When filter settings have been changed, the altered results can be imported in the workbench by right-clicking the original analysis result variant track in the workbench, and selecting "Variant Analysis Update". This which will generate a new variant track marked with (IVA update) (see Analysis using the plugin and the IVA web interface).