Ingenuity Variant Analysis plugin latest improvements
Ingenuity Variant Analysis 20.0
Released on December 11, 2019
Updated to be compatible with with CLC Genomics Workbench 20 and CLC Genomics Server 20.
Ingenuity Variant Analysis 4.4
Released on November 28, 2018
Updated to be compatible with with CLC Genomics Workbench 12 and CLC Genomics Server 11.
- The tool Add Information from Allele Frequency Community now annotates with ethnic group specific frequencies.
- The naming of the “general” frequency has been changed from “Community Frequency” to “AFC Frequency” to be in line with the behavior of IVA analyses.
- Each Map Reads to Reference step present in Ready-to-Use workflows under the Whole Exome Sequencing folder is now followed by a Remove Duplicate Mapped Reads step.
- All tools are now found in the Ingenuity Variant Analysis folder in the Toolbox.
Ingenuity Variant Analysis 4.3
Released on November 28, 2017
Updated for compatibility with new workbench and server releases.
Ingenuity Variant Analysis 4.2
Released on March 2nd, 2017
- Updated for compatibility with new workbench and server releases.
- In all workflows containing the tool “InDels and Structural Variants”, the value for the parameter “Minimum quality score” has been changed from “0” to “20” and the value for the parameter “Minimum consensus coverage” has been changed from “0.0” to “0.1”. This change does not affect the default values for these parameters, when running tool on its own.
Ingenuity Variant Analysis 4.1
Released on February 28, 2017
- Minor bugfixes and improvements.
Ingenuity Variant Analysis 4.0
Released on November 8, 2017
- A new ready-to-use workflow for identification of new and known pathogenic and cancer driver variants from cfDNA, called “Identify Somatic Variants from a Single cfDNA Sample Using IVA” was added in the toolbox under “Whole Exome Sequencing -> Somatic Cancer”.
- The “Identify and Interpret Causal Variants in Trio using IVA” workflows and the “Ingenuity Variant Analysis for Hereditary Diseases” tool got significantly improved and are now able to run all modes of inheritance simultaneously (recessive compound heterozygous, recessive homozygous, de novo, and dominant).
- All embedded workflows and tools now enforce diploid export for all chromosomes except for “X”, “Y”, and “MT” leading to the correct genotype display in the Ingenuity Variant Analysis web interface. The corresponding parameters have been removed from the user interface.
- The compatibility between input read regions, variants, and reference sequence is checked more consistently in Ingenuity Variant Analysis tools and workflows.
- Support for Variant Analysis Personal Genome Pipeline (i.e., “Single sample”) has been removed from the “Ingenuity Variant Analysis” tool.
- Support for the inheritance patterns “X-linked” and “Other/unknown” has been removed from the “Ingenuity Variant Analysis for Hereditary Diseases” tool.
- The “Identify and Interpret Causal Variants in Trio using IVA (TAS)” workflow to analyse trios enriched by target amplification has been removed, as have the “Family of Four” workflows.
- Uploaded samples are now assigned a random 32 bit family ID.
- Default output names of the “Ingenuity Variant Analysis for Hereditary Diseases” tool have been shortened.
- The history entries of the Ingenuity Variant Analysis tools have been improved.
Ingenuity Variant Analysis 3.1
Released on March 31, 2016
- When running the Ready-to-Use workflows that come with the plugin, Enforce diploid export has been exposed in the wizard and switched on as default option.
- In the drop-down options for “Analysis pipeline name”, “Personal genome” has been renamed to “Single sample”. Fixed a bug where the IVA plugin failed, when it was given a genome with a non-circular MT chromosome.
- The Ingenuity Variant Analysis Plugin is able to use the proxy settings specified in the Workbench preferences.
- In the Remove False Positive filter the Forward-reverse balance has been switched on for whole genome and whole exome sequencing data.