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.

Accepted file names for FASTQ

We expect files that conform to Illumina's naming convention. We can deal with multiple files, but we need the file names of each pair of paired-end files to be the same and only differ in the _N (or _RN). When parsing names of paired-end read files, we look for "foo_1.bar.fastq" and "foo_2.bar.fastq" where foo and bar need to be the same for the two pairs, and the only difference is the number. Alternatively, we also handle "foo_R1.bar" and "foo_R2.bar". 

Please keep in mind that when launching an analysis without UMIs, the file names should be R1 and R2, instead of R1 and R3, that usually correspond to the reads files.

In cases where there are more than two paired-end files per sample, all the paired reads should be provided: R1 with R2, R3 with R4, R5 with R6 and so on.

For further instructions in terms of naming conventions please refer to Illumina.

Uploading files

To upload files to VarSome Clinical or VarSome Pro, click on "Upload/View files". To open the file browser, click on "Select File(s)", and select all files that you want to upload. 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 checked, and the number of reads and of bases in reads are calculated and displayed for each file. Files can be deleted before or after upload. Files with status set to green can be used for a subsequent analysis and can be accessed at Launch analysis.

VarSome Clinical API

The platform comes with full API, allowing you to automate each step of data analysis process, including the data upload.