Data Upload

With VarSome Clinical you can process any kind of NGS data, be it an off-the-shelf or custom gene panel, an exome or whole genome. You can start the analysis either from FASTQ or VCF.

Uploading files

To upload files to VarSome Clinical, click on "Launch" > "1. Upload / View files" as shown in the following picture.

To open the file browser, click on "Select File(s)", and select all files that you want to upload. Files do not need to be from the same sample or in the same format. Once all files have been selected, the file names are displayed under the green icon "Select File(s)". To upload the files, click on "Start Upload".

View your uploaded files

Files are uploaded and analyzed, and the number of reads and bases in reads is calculated and displayed for each file. Files can be deleted before or after upload. Files with status set to dark green can be used for a subsequent analysis. 

You can organize your samples using Sample tags. For more information please visit Sample tags.

If you leave the page, the file upload process will stop. However, if the uploading reaches 100% (Uploaded) and VarSome Clinical is still validating the files on the right side, you can safely leave the page.

Additionally, if you wish to view the 'Analyses' table while the files are being uploaded, you can easily do so by opening it in a new tab.

Accepted input files

The accepted input files to run analyses on VarSome Clinical are either:

• FASTQ files only from Illumina or MGI sequencers
• VCF files which conform to the VCF standard, regardless of sequencing platform. You can upload VCFs containing only CNVs or a mix of CNVs and other SVs. The VCFs may contain the following types of variants: 
  • CNVs: deletion and duplication
  • Insertions
  • Inversions
  • Breakends 
  • Repeat expansions
  Users may also optionally upload an alignment BAM file for the VCF sample which can be used to visualize the coverage of the variants provided in the VCF file. 

Find more info in the documents Requirements for submitted FASTQ files and Requirements for submitted VCF files.