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      Analysis Actions menu

      You can see and retrieve various information about your sample(s) and the results of the analysis. This article lists the available options.

      You can access the list of available options in two ways by clicking on:

      i) the upper right corner of the analysis, from Dashboard.

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      ii) the "Analysis Actions" menu in the upper right corner of the variant table page. You can choose among a series of actions that allow you to retrieve information or generate different reports, provide an overview of your results, or further explore the analysis.

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      • SNVs & Indels: The results of the analysis. When clicked from the Dashboard, it takes you to the variant table.
      • Sample phenotype(s): Using these fields it is possible to add and modify the clinical description of the sample. You can choose this option if you want to provide phenotypes associated with your case from a drop-down menu or view the already selected ones. The phenotypes will be matched to the resulting variants. For more information please see: Phenotype Matching.
      • Sample/Analysis information: Opens a pop-up table with an overview of information about the sample, the sequencing (e.g. the capture method, number of reads and bases in reads, sequencer), and the analysis (e.g. the versions of the databases and the implemented pipelines and software).
      • Reuse sample files: This option is available if you wish to reuse an existing sample for a new analysis. A blue box message in the upper right corner of the page will let you know that you will receive an email when the input file(s) of the sample is/are again available for new analysis and which you can view in the "Upload / view files" page.
      • Gene coverage: When clicking on Gene Coverage, a new window will open showing a tree with the coverage per gene. Please note that only information for 100 or fewer genes is shown since the depiction of more genes would be impractical. If you wish to see coverage information for analyses with more than 100 genes, please use a gene list to limit the displayed results to 100 genes or fewer. The gene list can be selected when the new window opens by clicking on . If this option has been selected when analyzing a gene list, the tree will contain only the genes from that gene list. 

      Clicking on any gene will result in a tree of its transcripts and each transcript is also expanded to a tree showing the coverage of individual exons. Clicking on an exon will open a new tab, showing the read coverage from the corresponding .bam file.

      The following options concern the generation of different reports and can be useful when the user needs to check the quality of the sequencing in terms of coverage or retrieve information about the alignment. Please, refer to the article Report files to download for more information.

      • View QC report: You can view/download in DOCX or PDF format, a quality control report about your analysis. The report includes a list of information such as sequence technology, read alignment results, regions reported, coverage, number of identified variants by class, summary for Germline Variant Classification rules, and number of SNV found in coding regions. For more information, please refer to the article Quality Control Report.
      • View FastQC report: A quality control report for high throughput sequence data. For more information please see the documentation of the FastQC tool at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ and in the article FastQC Report. 
      • Coding coverage report: You can use a previously created gene list to produce an Excel document file reporting coverage information of the coding regions included in the analyzed gene list. This report can be exported for all component samples of a multi-sample analysis.
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      • Region list coverage report: You can use a list of regions of interest to produce an Excel document reporting coverage information. Contact us in case you want to add regions to your analysis.
      • Downloads: This option directs you to a new screen where you can see any files associated with this analysis that are ready to be downloaded.

        Sample Data File:
        • VCF file: A compressed (*.vcf.gz) vcf file will be downloaded with the results of the variant calling.
          • For sub-analysis (gene list analysis and algorithmic filters) there is a new option to “Generate VCF” that contains only the filtered variants.
        • BAM file: Download the bam file (the sample’s reads aligned against the reference genome) used in the analysis.
        • BAI file: The BAI file format is the index file of a BAM file. This is a companion file for your previous BAM file, which doesn't contain any sequence data but acts as an external table of contents allowing a computational tool to navigate in the BAM file and locate specific parts.
        Quality Control File:
        • QC report (PDF)
        • QC report (docx)
      • Download PGX report: PharmCAT is a pharmacogenomics clinical annotation tool that generates a report containing genotype-based prescribing recommendations. This option is available if a WGS and hg38 analysis has run.

      To execute a sub-analysis from the "Analysis Actions" menu:

      • Re-annotate analysis: ​Reannotating will not change the list of identified variants (we do not perform the calling again), it will simply re-annotate the same list of variants using the data available on the day of re-annotation. This means that some Germline and Somatic Variant Classifications might change if they are affected by newer data. Re-annotating an analysis is charged at 50% of the price of the original analysis. 
      • New Gene-List Analysis: This option will restart the analysis with the same sample using a previously generated gene list of selected genes or a gene list created from selected phenotype(s) or disease(s). It will appear as a sub-analysis of the initial analysis.
      • New Algorithmic Filter Analysis: Opens a new screen with the available algorithmic filters, as seen in section 3.2. Please click on the info icon, to get a description of each filter. Algorithmic filters create a snapshot of the parent analysis, with a filtered subset of variants, according to each Algorithmic filter. You can run a sub-analysis by choosing a filter from the list or you can ask for a custom-made filter. Please see Algorithmic FIlters.
      • New CNV sub-analysis: This allows you to annotate a VCF containing CNV variants found in the sample. It is necessary to upload a valid VCF first with CNVs to select it when launching this sub-analysis. 
      • Archive sample data: The analysis will be archived and a VCF file will be stored.
      • Delete FASTQ sample data: Allows to delete the fastq files used for the analysis. Once this option has been used, this will be disabled meaning that the files have been deleted from the server.
      • Delete BAM sample data: Allows to delete the bam file produced by the alignment during the analysis. Once this option has been used, this will be disabled meaning that the files have been deleted from the server.

       

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