Platform Updates VarSome Clinical

CNV Calling Enhancements

By Richard Meyer on September, 22 2021

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Richard Meyer


The v10.2 release of VarSome Clinical offers several novel features improving CNV detection, quality control and reporting. A new dynamic CNV browser offers an overall view of the call regions in their genomic context in every co-analysed sample. For detailed information, we recommend that users refer to the User Manual, which is accessible for download via the “Support & Manual” link in VarSome Clinical.

CNV call quality control - Explore the quality of each CNV call in depth

Additional quality data are displayed for each call that allow the user to assess result reliability. Each CNV call is assigned a set of three “traffic-lights”, which are colored green or red, depending on whether the CNV call meets the quality control criteria. These are:

  • Test sample coverage to ensure a minimum coverage of the test sample at the CNV call region when calling duplications. 
  • Number of reference samples to satisfy a minimum number (2) of samples from the reference set with a minimum coverage in the CNV call region. 
  • Camouflaged region overlap checks whether a CNV call falls within a genomic Camouflaged Region, which typically contain duplicated genomic sequences.


CNV Browser - Gain further insight with a dynamic visualization

A novel, bespoke, interactive CNV call visualization browser for every called CNV that offers:

  • Zooming to the CNV call region in the desired resolution.
  • Context genomic annotations including chromosomal location and exon and intron positions.
  • Local coverage information for all samples.
  • Easy linking to corresponding genomic regions in co-analyzed samples of the cohort.


CNV analysis QC report - Check sample quality in every analysis

Informative sample specific features that can affect CNV call quality are included in the analysis QC report:

    • Correlation to reference samples.
  • Reference sample listing.
  • Cohort sex data (if available). Unreliable CNV calls in sex chromosomes are filtered out.

If you would like to see a demonstration of VarSome Clinical's CNV features, you can book a time with our sales team here.

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