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. 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. 

Accepted file names for FASTQ

Files are expected to conform with Illumina's or MGI naming convention. 
Paired-end FASTQ files are required to have reads properly coordinated between them. Paired-end reads provided in a single FASTQ file are not accepted.

Illumina pair-end files will be considered pairs when the files will have 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. 

MGI pair-end files will be parsed 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)

For further instructions in terms of naming conventions, please refer to MGI Tech. 

In case were there are more than two paired end files per sample, all the paired reads should have the following naming structure: 
E12345_34_4321_L001_R1_001.fastq.gz 
E12345_34_4321_L001_R2_001.fastq.gz
E12345_34_4321_L002_R1_001.fastq.gz
E12345_34_4321_L002_R2_001.fastq.gz
E12345_34_4321_L003_R1_001.fastq.gz
E12345_34_4321_L003_R2_001.fastq.gz

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, or you can upload VCFs containing both types of variants.

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