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How to upload and set up files

Upload files

1. File format

It is possible to upload FASTQ, BAM or VCF NGS input files, regardless of the source of the sequencing. Compressed .gz files are also supported.

2. Source of files

  • Upload files from your computer

Select files from your computer and drag them to the dashed region.

  • Import files from BaseSpace Sequence Hub®

There are three simple steps: authenticate your Illumina BaseSpace Sequence Hub® account, authorize data sharing for your Varstation account and select the biosamples of interest. When selecting a biosample, all lanes from FASTQ and paired-end files for that biosample are already selected automatically.

Integration with BaseSpace® eliminates the time to load files as well as the need for a high capacity network, in addition to facilitating the flow between sequencers and software for Varstation secondary and tertiary analysis. With just one click, it is possible to upload all the biosample files in a single, safe and agile way.

3. Combination of files

If the files are selected from your computer, the system will try to combine the FASTQ with their respective paired-end to create each sample. The combination logic is based on the Illumina nomenclature, which prefixes “file_R1” for FASTQ and “file_R2” for its respective paired-end. That is, the system will search for files with the same prefix and will interpret that the pair “file_R1.fastq” + “file_R2.fastq” belong to the same sample.

For each FASTQ, the system accepts a single R2 paired-end. It is also possible to insert single-read FASTQ files, without the paired-end.

After selecting the files on your computer or through the integration module with BaseSpace® and clicking on “Continue”, you will access the routine configuration module.

If it is necessary to edit the sample combination, just access the button “Rearrange samples” to see how they were combined. You can make any corrections that may be necessary (separate or join files for each sample/patient).

Routine setup

1. Setup parameters

After selecting the files and clicking “Continue”, the next step is to set up the processing parameters. The files transferred to the system and the processing setup define a routine on Varstation platform.

For a simplified configuration the following information are required:

1. Reference genome: hg19*;

*currently is the only one available, we will make hg38 available soon.

2. Sequence platform: Illumina or Ion torrent;

3. Library type: Amplicon or Captura;

4. Analysis type: Germline/hereditary or Tumor/somatic;

5. Target region of the analysis: From .bed file (text file format that usually contains chromosome, start and end of the target regions) or from selection of specific genes (type or paste a comma separated list of genes) or do not insert target region.

After selecting the 5 parameters, the corresponding processing workflows will be available on the right for consult. These are workflows validated by our bioinformatics team and that load automatically according to the selection of platform, library and type of analysis.

If you need to repeat this setup in future routines, we also offer the possibility to name and save the pipeline (setup). In the next routine, this setup will be available for you to select, without having to set it up again.

2. Offering pipelines

We offer validated pipelines, which correspond to some kits available on the market:

  • Exome Agilent SureSelect Human All Exon V5
  • Exome Agilent SureSelect Human All Exon V6
  • Exome Agilent SureSelect Human All Exon V7
  • Exome Agilent SureSelect Clinical Research Exome V2
  • Exome Illumina TruSight One Expanded

If it is necessary to create a customized pipeline for a specific need, just contact our team to quote. (support@varstation.com)

3. Sample feedback

Reference genome: hg19 (padrão)

Sequence platform: Illumina

Library preparation: Capture

Analysis type: Germline/Hereditary

Genes of interest: BRCA1, BRCA2, CDH1, PALB2, PTEN, STK11, TP53

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