Launching new analysis

To start a new analysis, click on 'Launch analysis'. Launching a germline or somatic analysis has been separated as different options on the user interface. Υοu can select one of the available options:

  • Germline Analysis from FASTQ
  • Germline Analysis from VCF
  • Somatic Analysis from FASTQ (AMP Included)
  • Somatic Analysis from VCF (AMP Included)
  • Tumor - Normal analysis (AMP Included)

For Germline samples

  • Germline Analysis from FASTQ

 

  • Germline Analysis from VCF

 

For Somatic Samples

  • Somatic Analysis from FASTQ (AMP Included)

  •  Somatic Analysis from VCF (AMP Included)

Note: Somatic samples cannot be used in multi-sample analyses

For Germline analyses fill in the form:

  • Sample Identifier: Write the name of your sample here. The sample ID must not contain information about patient identity.
  • Description: A description of your analysis. This field is optional.
  • Select files to use: Click on Select File(s) to use to choose the sample(s) that you want to analyse. Usually, two files if you are uploading paired-end FastQ files and one file if you are uploading VCF. Files must be compressed and have the .gz extension.
  • Phenotype and Disease Information: A description of your sample phenotype/disease using HPO terms. These terms, can be used to create a gene list and filter the variant analysis for the genes matching the selected phenotypes and/or diseases.
launch-fastq-pheno
  • Launch: Choose whether to analyse i) a single sample; ii) several independent samples (each of them will be shown as a separate analysis, they are just launched together for convenience) or iii) a multi-sample analysis, run a joint variant calling tool on all samples at once, which can increase sensitivity and decrease false positive rate over analysing each sample separately. The results of all samples will be displayed together in a single table (e.g. family trio)
  • Capture/Amplicon Kit: Select the capture, amplicon, whole genome library preparation method or kit corresponding to your analysis. If you are uploading fastq files, this is important information. The capture/amplicon kit details will be used to calculate the coverage of the coding regions included in the kit. This information will be shown later in the Quality Control (QC) Report. If you do not know what kit was used to prepare the capture/amplicon library, you should choose "generic other capture kit" or "generic other amplicon kit".
  • Ethnicity: If needed, specify one of the ethnicities proposed by Gnomad. E.g. when European is chosen, the allele frequency shown in the final results will correspond to the European population.
  • Sequencer: This is the Illumina Sequencer machine model (e.g. MiSeq, HiSeq 2500 ...) used to produce the data. This information will be reported later in the Quality Report and in the Sample information. It can be useful to, for example, write the diagnostic report.
  • Reference Genome: Choose the reference genome the reads will be aligned to.

  • Variant list: Do you really want to see all the variants? If you also need the variants that did not pass the quality filters, then you should choose "Variant list will contain all variants". By default, only the high quality variants will be reported. Selecting "Variant list will contain all variants" will increase the amount of annotated variants and it could slow down the analysis.
  • Full or Gene list analysis: Do you need to restrict your in-silico variant analysis to a gene list? If you choose "Gene list analysis", the final results will only contain variants found in gene transcripts contained in that list (500 bp upstream and downstream of each transcript are included).
  • Click Start to launch your analysis.

For Somatic analyses fill in the form:

  • Sample information: Write the name of your sample here. The sample ID must not contain information about patient identity.
  • Description: A description of your analysis. This field is optional.
  • Click on Select File(s) to use to choose the sample(s) that you want to analyse. Usually, one file if you are uploading vcf files and a pair of files for fastq. Please note multi-sample vcfs are not allowed for tumor samples. The vcf files must be compressed and have the .gz extension.
  • Tissue Type: Specify the tissue type of your sample. This field is optional, however we encourage you to fill it in, as this information gets considered for the annotation with Cancer databases. 
  • Cancer Type: Specify the sample’s type of cancer. This field is optional, however we encourage you to fill it in, as this information gets considered for the annotation with Cancer databases. 
  • Age: Specify the sample’s individual age (in years). This field is optional, however we encourage you to fill it in, as this information gets considered for the annotation with Cancer databases. 
  • Sex: Specify the individual’s sex.  This field is optional, however we encourage you to fill it in, as this information gets considered for the annotation with Cancer databases. 
  • Ethnicity: If needed, specify one of the ethnicities proposed by Gnomad. For example, when European is chosen, the allele frequency shown in the final results will correspond to the European population. This field is optional, however we encourage you to fill it in, as this information gets considered for the annotation of Cancer databases. 
  • Reference Genome: Choose the reference genome used to create the vcf file.
  • Full or Gene list analysis: Do you need to restrict your in-silico variant analysis to a gene list? If you choose "Gene list analysis", the final results will only contain variants found in gene transcripts contained in that list (500 bp upstream and downstream of each transcript are included). 
  • Click Start to launch your analysis. Your samples will be uploaded to VarSome Clinical’s servers and the analysis will start automatically.

Tumor-normal analysis (AMP Included)

A tumor - normal analysis requires a tumor sample and a somatic normal as a control, coming from the same individual. Τhe results only show variants present in the tumor sample that are absent from the control (with AMP annotation included). Fill in the fields as described above, giving the information for the tumor and normal sample in the respective sections.