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.