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 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 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 or MGI sequencers
• VCF files with standard-compliant format, regardless of sequencing platform 
• BAM files for alignment visualization when launching an analysis starting from VCF

Accepted file names for FASTQ

We expect files that conform to Illumina's or MGI naming convention.

When providing paired-end FASTQ files, we require that reads are properly coordinated between them. Paired-end reads provided in a single FASTQ file are not accepted.

For Illumina pair-end files, we will consider pairs to be files with the exact same name except for the number of the read, for example SampleName_S1_L001_R1_001.fastq.gz and SampleName_S1_L001_R2_001.fastq.gz. We accept files in which the read number is specified alone (for example SN1234_S1_L001_1.fastq.gz and SN1234_S1_L001_2.fastq.gz) or with an “R” before the number (for example SN5678_S1_L001_R2.fastq.gz and SN5678_S1_L001_R1.fastq.gz). For further instructions in terms of naming conventions please refer to Illumina.

For MGI pair-end files, we will parse the files as follows: [flow cell ID]_[lane ID]_[barcode ID]_(optional_id)_[read 1/2].fastq.gz and we accept the number of the read to be specified alone (for example, 12345_L02_48_1.fastq.gz and 12345_L02_48_2.fastq.gz) or with an “R” before the number (for example, 6789_L02_56_R1.fastq.gz and 6789_L02_56_R2.fastq.gz)

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.

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.