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VarSeq 2.0.1 Release Notes

New Product Add-Ons

  • VSClinical ACMG Guidelines work-flow now available as an add-on licensed product to VarSeq! This product supports the evaluation of variants from your VarSeq project within a guided work-flow that assists in the scoring of the ACMG criteria for classifying variants.
  • New splice prediction and functional prediction algorithms are also included in VSReports and VSClinical. Splice predictions will be part of any newly run gene annotation algorithm when the appropriate add-on license is available. Function prediction and conservation scores can be found under the Secure Annotation location when adding annotations.

New Features

  • After importing data into your project, you can edit the sample fields including the BAM file associated with each sample. Go to File > Set Sample Fields… to use this feature. This also allows adding in the parental relationships or correcting the naming of samples. After sample fields have been edited, any algorithm dependent on this data will be re-run (including this like coverage statistics and CNV analysis).
  • You can now use HPO IDs directly in our imported phenotype list field as well as our Phenotypes input line for the PhoRank algorithm. For example, you can type HP:0000717 instead of “Autism”.
  • When curating custom annotation files, you can now lift over coordinates from GRCh37 to GRCh38 and visa-versa. This is available in the Advanced Options of the Covert screen.
  • A function was added to the Convert Wizard called, unquote that allows the user to remove surrounding single or double quotation marks.
  • The gene and transcript annotation algorithm has been updated to have a system-wide mechanism for specifying a default transcript to use when reporting the Clinically Relevant Transcript. The current default transcript heuristic is overridden with the transcript that has been used by the majority of submitters to ClinVar for 438 genes. Using VSClinical, the system wide default transcript for a gene can be updated and saved.
  • During gene and transcript annotation, insertions and deletions will move to their right-aligned position before being projected into the transcript and the protein product. While this was occurring in our HGVS protein description before, it now is consistently done for our HGVS coding description as well as the sequence ontology and effect of the variant. The result is a consistent HGVS that matches external sources like ClinVar.
  • The CNV Caller on Target Regions algorithm has been updated with a slight modification to how it performs some of the probability calculations to be more accurate in the context of calling CNV with just a few target regions. Results will largely agree with 1.5.0, but more CNVs may be called in cases where the evidence was very near the threshold.
  • The CNV Caller on Target Regions algorithm offered an option to Normalize sex chromosomes separately based on inferred gender. When this option was selected, the chromosomes would be normalized only with other sample values with the same chromosome. Now, this option is calledNormalize sex chromosomes using only controls with matching sex which selects references of matching sex and thus does not normalize the sex chromosomes separately. This improves the accuracy of calling CNV events in X and Y chromosomes when an adequate number of gender-matched reference samples are available.

Bugs Fixed

  • When running VarSeq on a Windows Server 2008 machine through remote desktop, the browser tab would sometimes appear as a black rectangle and would crash VarSeq when maximizing VarSeq. This has been resolved with a fix for a third-party library.
  • VarSeq can now compute coverage over regions in the X and Y chromosomes when the BED files that define the regions list the X and Y chromosomes in lower case text.
  • Previously, projects that were created in VarSeq before version 1.5.0 and used LoH calculation would crash when opened up in VarSeq 1.5.0. This has been resolved so that older projects using LoH can be opened safely.
  • An error is now supplied when running the “Add Coverage Regions…” algorithm and the sample BAM paths are broken.
  • Projects without the MT chromosome caused a crash when filtering for variants within the MT chromosome. Filtering on missing chromosomes no longer causes a crash.
  • Opening project templates that used an annotation source that the user has deactivated after the deactivation caused a crash. This crash is fixed and an error is supplied to alert the user that a different annotation source is needed.
  • Exporting a subset of the Coverage Regions table without the genomic Regions column to Excel or TSV resulted in blank fields. This has been resolved and arbitrary sets of columns can be exported from any table.

Polishes

  • The integrated web browser and VSClinical now scale appropriately to the DPI setting of your desktop, responding to higher scaling factors on a per-monitor basis.
  • Creating a project from a template names the primary imported source based on the new project name versus the template name. This shows up with selecting fields for things like the Compute Fields algorithm.
  • The HPO and GO bundled ontology files have been updated to the latest snapshots available from these primary sources.
  • In the import wizard, the Add Folder feature that recursively scans sub-folders for importable VCFs now has a concealable status dialog to provide feedback during the potentially long-running operation.

Additional 2.0.1 Notes

Bugs Fixed

  • Creating projects from existing templates unintentionally added the splice prediction algorithm option to existing gene annotations. This would then stop the algorithm from running if the current user was not licensed for VSReports or VSClinical. This has been fixed so newly created projects from existing templates will be created without the splice predictions and run to completion. When adding gene annotations to a project, the choice to use the splice site prediction algorithms will be available if that feature is licensed.
  • VSClinical recommendations for BS1 are now aware of quality flags so as not to recommend scoring BS1 when the population catalog data may not be reliable.

Polishes

  • Update the Multiple Sequence Alignment view in VSClinical to have better column overlay positioning when the browser is zoomed in.
  • Links embedded in the OMIM details content dialog now open a browser in a separate tab instead of changing the VSClinical tab to the opened page.
  • The chromosome name is displayed alongside the accession in the Variant Details card of VSClinical.
  • Better edge case handing for HGVS p. notation for transcripts that have no stop codon in the reference sequence.
Updated on January 21, 2021

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