The primary goal of this release is to improve the speed with which the variant table loads as well as the time taken to load variant data when switching from one variant to another and to improve the responsiveness of Dynamic Filters.

Additionally, we have incorporated a few amendments that were requested by some of our customers that aim to improve usability.

Important: If you have previously customized the column order on the results table, your changes will have been lost and you will need to reset the first time you load an analysis.

Highlights

• The variant table loads more quickly

• More responsive Dynamic Filters

• Custom classification for AMP and CNV

• Improved variant table search

• Additional API endpoints.

Variant Table Updates

Improved Search Option

The search tool on the variant table has been brought into line with VarSome search. You can now search by gene, chromosome, position and range etc. Please find further details on search options available in the Variant Table help article.  

Custom Classifications.

As with ACMG, you can now add and save custom classifications for AMP. You can also custom classify CNVs if a copy number is present.

Zygosity Column

For heterozygous genotypes, we now show a different icon depending on whether the underlying VCF file has 0/1 or 0|1 for which we’ll show , or 1/0 or 1|0 for which we’ll show . Please note that this does not imply that the variants are phased. Only the 1|0 and 0|1 zygosity values indicate phasing, the 1/0 and 0/1 notations are equivalent. We are only making this change now as the first step in our upcoming support for phasing. 

Filtered Variants

Previously, when a filter was applied it would say “x no. of variants filtered out”. Now more detailed information is shown that shows filtered variants, the actual values and the filter used.

Exporting filtered variants to Excel

• If the exclusion criterion has been used for a filter, it is now displayed in the excel file of exported variants on the tab “Filters used per variant”:

The word  “excluded” refers to the filter, not the variant.

• The variant  in the exported Excel spreadsheet is now a link to the variant’s page on VarSome.

CNV Transcripts

Canonical transcripts are now highlighted in the CNV results in red:

Filters

We have added two new buttons on the filters pane:

1. Reset Filters
2. Apply Filters

Filters will no longer be automatically applied. This enables you to edit and reorder your filters before applying them, as well as see how many variants would be removed if the filter were applied. Hit the "Apply" button to apply your chosen filters. The “Reset Filters” button can be used to clear the list of selected filter sets. 

Multiple sorting

The list of variants can now be sorted by multiple columns. A pop-up window will appear and multiple columns of interest can be selected in order to sort the variants in ascending or descending order.

It is now possible to sort by multiple columns. By selecting this option, a pop up appears enabling you to add “levels” of sorting.

Continual Improvements

The “Filtered Variants” button has been moved to the green boxes above the results table:

API Documentation

The API documentation is now grouped together by type and several additional API endpoints have been added. Please see the API documentation that clearly shows these improvements. 

Support

All of these changes have been reflected in the updated User Manual available in the “Support & Manual” section of VarSome Clinical. 

As ever we hope you find these changes & improvements helpful, we’d love to hear any suggestions you may have, support is available as usual from support@varsome.com

The VarSome Team.