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 "Upload/View files". 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 of bases in reads is 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.

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

Accepted input files

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

• FASTQ files only from Illumina sequencers or
• VCF files with standard-compliant format, regardless of sequencing platform. There is also support directly for VCF files from IonTorrent platform (ThermoFisher).

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.gz" and "foo_2.bar.fastq.gz" 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". When providing paired-end fastq files, we require that reads are properly coordinated between them. Paired-end reads provided in one single fastq file are not accepted.

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.

Requirements for submitted VCF files

VarSome Clinical accepts VCF files for SNPs/INDEL and CNV annotation. You can upload VCFs containing only SNPs/INDELs or CNVs, but you can also upload VCFs containing both types of variants.

For further information, please refer to the corresponding article Requirements for submitted VCF files.