Platform Updates

BaseSpace Integration with VarSome Clinical

By Richard Meyer on June, 9 2021

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Richard Meyer


We are proud to announce that Illumina BaseSpace integration is now available in VarSome Clinical. By linking up your accounts, you will be able to transfer your files directly from BaseSpace to VarSome Clinical, saving you the need to download your exomes and genomes directly to your computer.


This new feature can be accessed by clicking on the “Illumina BaseSpace” option displayed in the drop down menu shown when you hover over your user name.


After you click on “Connect your BaseSpace Account” you will be automatically redirected to Illumina’s site in order to login to your account.

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Your projects will then synchronize with VarSome Clinical after you have granted the necessary permits.

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Please note: if you do not grant access to VarSome, then your projects cannot synchronize and you will be unable to transfer files.


This new functionality will allow you to download the FASTQ files directly to VarSome Clinical. To do this, please, click on the “Download” button to start downloading the reads into VarSome Clinical.

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Please, wait a few minutes while the files are being downloaded. The downloading time will depend on the size of your data.

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Once the download is complete, the status of the file will change from “Not available” to “Available”, meaning that the FASTQ files are accessible from the “Upload/View files” page and can be used to launch analyses (germline or somatic) from FASTQ. 


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Please note that any file that has been previously imported from BaseSpace to VarSome Clinical will have a status of “Available”. If the file has already been used in an analysis, in order to analyze it again you will need to find the sample that contains it and select the option “Re-use sample files”

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We hope you enjoy this new functionality. As always, if you require any additional help we are always happy to help. And if you are not already a VarSome Clinical user, let us know if you would like to find out more.

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