---
title: Sample cross-referencing
description: "VarSome Clinical comes with powerful sample cross-referencing, which links all your samples together on the variant level. It can be found in each sample's     tab and it reports two things: 1. Shows"
---

[Skip to content](https://docs.varsome.com/en/sample-cross-referencing#main-content)

English

Show submenu for translations

[Submit a Support Request](https://docs.varsome.com/en/kb-tickets/new?hsLang=en) [Customer portal](https://docs.varsome.com/support-requests?hsLang=en)

[![varsome-new.png\]](https://docs.varsome.com/hs-fs/hubfs/varsome-new.png?height=40&name=varsome-new.png)](https://docs.varsome.com/en?hsLang=en)

- Editions
  
  Show submenu for Editions

    - [VarSome.com](https://landing.varsome.com/varsome)
    - [VarSome Clinical](https://landing.varsome.com/varsome-clinical)
    - [VarSome Premium](https://landing.varsome.com/varsome-premium)
    - [VarSome API](https://landing.varsome.com/varsome-api)
    - [VarSome Insights](https://landing.varsome.com/varsome-insights)
- About
  
  Show submenu for About

    - [The Company](https://saphetor.com/)
    - [Contact Us](https://landing.varsome.com/contact)
    - [Distributors](https://landing.varsome.com/distributors)
    - [Become a Partner](https://landing.varsome.com/become-varsome-partner)
    - [Community](https://varsome.com/community-contributions/)
    - [Cite VarSome!](https://varsome.com/about/general/varsome-citations/)
- Resources
  
  Show submenu for Resources

    - [Datasources](https://varsome.com/datasources/)
    - [Germline Classification](https://varsome.com/about/resources/germline-implementation/)
    - [Somatic Classification](https://varsome.com/about/resources/somatic-implementation/)
    - [CNV Classification](https://varsome.com/about/resources/sv-implementation/)
    - [Help Center](https://docs.varsome.com/)
    - [Library](https://landing.varsome.com/whitepapers)
    - [IVDR](https://landing.varsome.com/ivdr-whitepaper)
    - [Legal & Compliance](https://docs.varsome.com/en/legal-compliance)
- Blog
  
  Show submenu for Blog

    - [Platform Updates](https://updates.varsome.com/en)
    - [Company News](https://news.varsome.com/en)
    - [VarSome Annotated](https://blog.varsome.com/annotated)

Open main navigation

Close main navigation

- Editions
  
  Show submenu for Editions

    - [VarSome.com](https://landing.varsome.com/varsome)
    - [VarSome Clinical](https://landing.varsome.com/varsome-clinical)
    - [VarSome Premium](https://landing.varsome.com/varsome-premium)
    - [VarSome API](https://landing.varsome.com/varsome-api)
    - [VarSome Insights](https://landing.varsome.com/varsome-insights)
- About
  
  Show submenu for About

    - [The Company](https://saphetor.com/)
    - [Contact Us](https://landing.varsome.com/contact)
    - [Distributors](https://landing.varsome.com/distributors)
    - [Become a Partner](https://landing.varsome.com/become-varsome-partner)
    - [Community](https://varsome.com/community-contributions/)
    - [Cite VarSome!](https://varsome.com/about/general/varsome-citations/)
- Resources
  
  Show submenu for Resources

    - [Datasources](https://varsome.com/datasources/)
    - [Germline Classification](https://varsome.com/about/resources/germline-implementation/)
    - [Somatic Classification](https://varsome.com/about/resources/somatic-implementation/)
    - [CNV Classification](https://varsome.com/about/resources/sv-implementation/)
    - [Help Center](https://docs.varsome.com/)
    - [Library](https://landing.varsome.com/whitepapers)
    - [IVDR](https://landing.varsome.com/ivdr-whitepaper)
    - [Legal & Compliance](https://docs.varsome.com/en/legal-compliance)
- Blog
  
  Show submenu for Blog

    - [Platform Updates](https://updates.varsome.com/en)
    - [Company News](https://news.varsome.com/en)
    - [VarSome Annotated](https://blog.varsome.com/annotated)
- English
  
  Show submenu for translations
- [Submit a Support Request](https://docs.varsome.com/en/kb-tickets/new)
- [Customer portal](https://docs.varsome.com/support-requests)
- [Contact us](https://docs.varsome.com/en/kb-tickets/new)

[Contact us](https://docs.varsome.com/en/kb-tickets/new?hsLang=en)

 How can we help you?

- There are no suggestions because the search field is empty.

1. [VarSome Help Center](https://docs.varsome.com/en?hsLang=en)
2. [Analysis of the results](https://docs.varsome.com/en/analysis-of-the-results?hsLang=en)
3. [Results](https://docs.varsome.com/en/analysis-of-the-results?hsLang=en#results)

# Sample cross-referencing

VarSome Clinical comes with powerful **sample cross-referencing**, which links all your samples together on the variant level. It can be found in each sample's   ![](https://docs.varsome.com/hs-fs/hubfs/image-png-Jan-10-2025-12-08-34-9177-PM.png?width=88&height=45&name=image-png-Jan-10-2025-12-08-34-9177-PM.png)  tab and it reports two things:

1\. Shows the number of samples across all VarSome Clinical users where this specific variant has been identified.

2\. Highlights other samples within your account or group that also contain this variant.

Please note that a variant identified in an archived sample will still appear as a metric in the ![](https://docs.varsome.com/hs-fs/hubfs/image-png-Jan-10-2025-12-08-34-9177-PM.png?width=88&height=45&name=image-png-Jan-10-2025-12-08-34-9177-PM.png) tab, along with its zygosity, allelic balance (when available), and any associated phenotype (if the analysis in which it was identified is linked to a phenotype).

This information is updated daily. The number of homozygotes and heterozygotes in VarSome Clinical for the variants are shown, but only sample IDs of samples analyzed **by you** **and your group** are reported. 

Please note that Variants with a gnomAD frequency greater than 5% are not considered for sample cross-referencing. This was done in order to reduce the loading time of the results.

[![](https://docs.varsome.com/hs-fs/hubfs/image-png-Jun-06-2025-12-03-09-5309-PM.png?width=670&height=140&name=image-png-Jun-06-2025-12-03-09-5309-PM.png)](https://docs.varsome.com/hubfs/image-png-Jun-06-2025-12-03-09-5309-PM.png?hsLang=en)

 

[![](https://docs.varsome.com/hubfs/image-png-Aug-09-2022-01-18-03-31-PM.png)](https://docs.varsome.com/hubfs/image-png-Aug-09-2022-01-18-03-31-PM.png?hsLang=en)

**Did you know?**

Sample cross-referencing enables you to compare your past and current cases, compare patient's phenotypes and ultimately [increase the diagnostic yield](https://blog.varsome.com/increasing-the-diagnostic-yield-with-varsome-clinical?hsLang=en).

Moreover,  VarSome Clinical allows you to [share your data with other institutions](https://docs.varsome.com/variant-sharing-among-institutions?hsLang=en) if both parties consent in writing.

[![vclin-only-cropped](https://docs.varsome.com/hs-fs/hubfs/vclin-only-cropped.jpg?width=670&name=vclin-only-cropped.jpg)](https://saphetor.com/varsome-editions/varsome-clinical/)

 

- [Registration & Billing](https://docs.varsome.com/en/registration-billing?hsLang=en#main-content)

    - [User account management](https://docs.varsome.com/en/registration-billing?hsLang=en#user-account-management)
    - [Storage management](https://docs.varsome.com/en/registration-billing?hsLang=en#storage-management)
    - [Pricing and Billing](https://docs.varsome.com/en/registration-billing?hsLang=en#pricing-and-billing)
    - [VarSome Clinical Tokens](https://docs.varsome.com/en/registration-billing?hsLang=en#varsome-clinical-tokens)
- [Management of Samples and Analyses](https://docs.varsome.com/en/management-of-samples-and-analyses?hsLang=en#main-content)

    - [Uploading files](https://docs.varsome.com/en/management-of-samples-and-analyses?hsLang=en#uploading-files)
    - [Managing Samples](https://docs.varsome.com/en/management-of-samples-and-analyses?hsLang=en#managing-samples)
    - [Managing Workflows](https://docs.varsome.com/en/management-of-samples-and-analyses?hsLang=en#managing-workflows)
    - [Launching analyses](https://docs.varsome.com/en/management-of-samples-and-analyses?hsLang=en#launching-analyses)
- [Analysis of the results](https://docs.varsome.com/en/analysis-of-the-results?hsLang=en#main-content)

    - [Analyses](https://docs.varsome.com/en/analysis-of-the-results?hsLang=en#analyses)
    - [Results](https://docs.varsome.com/en/analysis-of-the-results?hsLang=en#results)
    - [Filters](https://docs.varsome.com/en/analysis-of-the-results?hsLang=en#filters)
    - [Reporting](https://docs.varsome.com/en/analysis-of-the-results?hsLang=en#reporting)
    - [Quality Control](https://docs.varsome.com/en/analysis-of-the-results?hsLang=en#quality-control)
- [Legal & compliance](https://docs.varsome.com/en/legal-compliance?hsLang=en)
- [FAQ & Troubleshooting](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en#main-content)

    - [Troubleshooting](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en#troubleshooting)
    - [General](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en#general)
    - [Filters](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en#filters)
    - [User Interface](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en#user-interface)
    - [Pipelines](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en#pipelines)
    - [Features](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en#features)
- [Scientific articles](https://docs.varsome.com/en/scientific-articles?hsLang=en)
- [VarSome API](https://docs.varsome.com/en/varsome-api?hsLang=en)

[![VarSome Logo](https://docs.varsome.com/hs-fs/hubfs/VarSome%20Logo.png?width=200&height=47&name=VarSome%20Logo.png "VarSome Logo")](https://varsome.com)

**Resources**  
[Query Examples](https://varsome.com/about/resources/examples/)  
[Germline Classification](https://varsome.com/about/resources/germline-implementation/)  
[Somatic Classification](https://varsome.com/about/resources/somatic-implementation/)  
[White Papers & Other Resources](https://varsome.com/library/)  
[Cite VarSome](https://varsome.com/about/general/varsome-citations/)  
[System Status](https://status.saphetor.com/)  
[Help Center](https://docs.varsome.com/en?hsLang=en)

<https://www.linkedin.com/showcase/varsome/> <https://twitter.com/varsome?lang=en> <https://www.youtube.com/channel/UCwEorND5-pl_9juijC1YGQA> <https://landing.varsome.com/varsome-clinical?hsLang=en>

**Legal**  
[Terms of Use](https://varsome.com/information/legal/terms/)  
[Privacy Policy](https://varsome.com/information/legal/privacy/)  
[Information Security](https://varsome.com/information/legal/information-security/)

Copyright © 2025, Saphetor SA