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VarSeq 2.1.0 Release Notes

New Features

  • You can now import CNVs from external sources in text or VCF file format. This requires the VS-CNV module and supports the CNV based annotation, filtering, plotting and reporting capabilities. See Importing Regions and CNVs for more details.
  • A new VSReport called VSClinical ACMG Gene Panel Template is available that can pull in on-demand the interpretations done in VSClinical. It also has a CNV section that can be configured to pull in classification and interpretations from a CNV Assessment Catalog.
  • On import of VCF files, you can now lift-over to the assembly of the project by specifying the “Assembly of Input Files” for your selected VCFs. This allows you to start using GRCh38 projects for example, by knowing you can still import historical GRCh37 data. Similarly, you could import GRCh38 data into existing GRCh37 projects.
  • New commands were added to vspipeline that allow users to list field titles, change field title visibility in projects, and to export fields from the vspipeline command line.
  • When exporting of VCFs, field names that have been changed to user-defined in the table will be used.
  • Our integrated web browser has been updated to be based on Chromium 65, which will improve performance of the ACMG Guidelines workflow. This also resolves a couple system-specific compatibility issues reported by users.
  • The Coverage Statistics algorithm has a new option to only include reads with proper pair alignments (with the BAM 0x02 flag). This option is not enabled by default, but may be desirable in some situations where a large number of untrustworthy mappings are influencing the coverage statistics.
  • The Copy Number calling algorithms were updated to use a faster and near-equivalent segmentation algorithm strategy, improving run-times for exomes and gene panels with many targets in a small genomic region. In testing, this improvement causes no loss in sensitivity of true positive events. Adding a new CNV algorithms to a project will use the new strategy by default unless the option to use the slower optimal segmentation algorithm is selected in the advanced parameters tab. Existing templates will run with the previous strategy until they are manually updated.

Bugs Fixed

  • In the VarSeq tables, the header name of a source that was being updated was at times out of date. This was corrected to show the proper titles during the update process.
  • The feature to support “appending” input files with same sample names was broken in VarSeq 2.0.2 when there were more than one sample in the import. The merge process was updated to again support this import scenario. It also was improved to not merge variants with conflicting genotypes.
  • When using Assessment Catalogs, if you edit or write an assessment and changed the current variant without saving, you are prompted if you want to save changes for the previous variant. If you chose to “Save” changes, the currently selected variant was being updated to the Ref/Alt of the just-saved variant leaving the Assessment Catalog window in a bad state. This has been fixed and prevents the possibility of creating an assessment on an invalid variant.
  • Variants that were finalized using the ACMG workflow were occasionally counted twice on the ACMG Guidelines start screen due to registering multiple clicks during the finalization step. Changes were made to not include multiple finalizations on the same variant.
  • VSClinical was crashing when encountering project paths that included unicode character formatting. Changes were made to support running VSClinical from a program path containing unicode characters on Windows.
  • Projects created in older versions of VarSeq would cause a crash when opened in VarSeq 2.0.2 if there were significant differences in the selected inputs or certain complex workflows. This was corrected to adjust for the mismatch in input size and improve the order algorithms run.

Polishes

  • Due to the confusion it caused, we deprecated the reference genome assembly that contained the hg18 mitochondrial and auto-update all projects to use the new “GRCh37 (hg19)” reference. Older annotations are also now hidden by default to prevent accidental usage.
  • VarSeq now does a better job scaling the user interface when running on Windows computers with high DPI settings (high resolution monitors with scaling factors applied).
  • Starting VarSeq for the first time on a new computer prompts for you to consider where you would like to locate the AppData folder. You can find this prompt under Tools -> Move AppData Folder….
  • A number of improvements and feature polishes have been added to VSClinical’s ACMG Guideline workflow:
    • Creating a New Evaluation does a query of each variant against the VSClinical Catalog and reports the status of each variant before starting.
    • The Golden Helix Classification Prediction score now starts out in a more intuitive state when no questions are answered and has improved handling of a mix if answered and un-answered scoring questions.
    • Finalizing a sample allows the option to accept un-finalized variants that were previously classified or not.
    • The Studies tab now has a “Search PubMed” button to allow searching for literature that references the current variant or other variants in the same amino acid.
    • On the gene table of classified variants for the current gene, you can now click on the Last Seen date to look at the details of classifications made by your lab on previous samples.
    • Copying in text or references with the [+] copy icon no longer triggers a hiding of the list of ClinVar assessments on the studies tab.
    • Improved support for adding variants using Chr:Pos Ref/Alt syntax in the Add Variants dialog.
    • Manually added variants are now checked for previous classifications and have their position highlighted in any GenomeBrowse tab.
    • Finalized evaluations do not have their auto-recommendation updated so they reflect the state of the recommendation engine when they were finalized.
    • Newly created VSClinical ACMG Assessment Catalogs have a “Variant Tags” field that saves the names of the Record Sets to Report that were selected for a variant when it is finalized.
    • The PS4 criteria was added for case/control study evidence to the Clinical criteria section.
  • A number of improvements for the VSClinical Variant Dashboard:
    • Before any rows are selected, a helpful message is displayed
    • When selecting multi-allelic variants, a new allele toggle allows viewing each alternate allele in the dashboard.
  • The default Clinically Relevant transcript has been updated in a number of genes to reflect the latest ClinVar analysis of the most commonly used transcript in clinical submissions.
  • The HGVS notation produced by our transcript annotation algorithm and displayed in VSClinical shortens very long insertions/deletions using abbreviated notation when changing more than 5 amino acids. Also variants affecting the start codon and the stop codon have had their HGVS notation improved to be more informative.
  • When using the “Add CNVs” feature to run the VS-CNV algorithm, VarSeq no longer prompts for you to run the LoH algorithm, as it was not providing a useful improvement in most cases.
  • The option to include certain Record Sets in reports is now only shown if Record Sets were assigned when creating an ACMG workflow in the VSClinical ACMG Options dialog.
  • New error messages were added to alert users to whether there was an algorithm failure due to file permissions and where the file in question is located.
  • When exporting variants or other tables from VarSeq, you can no longer specify invalid file name characters for your exported file name.
  • Saving or updating assessment catalogs entries not produces more detailed log message that includes custom keys like the sample name associated with the modified record.
Updated on January 21, 2021

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