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Generate reports

Report generation is started for a sample if the following conditions are met:

  1. There is at least one active report template added to the system that has at least one added block and is applicable to the sample type. The template can be applicable to tumor, normal, or any samples. In addition, a report template that meets all of the above conditions must be added to the system before the sample analysis was complete. If you added or updated a report template after the sample analysis completion and you want to generate or update the corresponding report for this sample, reprocess the sample from the "Generate reports" stage.
  2. The sample analysis workflow includes alignment and one of the following analysis stages: "Somatic SNVs/Indels discovery" for a tumor sample; "Germline SNVs/Indels discovery" for a non-tumor or single tumor sample; or "Copy number variations discovery". The presence of other analysis stages may only affect the generation of specific reports or their content.
  3. The sample analysis has been successfully completed (i.e. all stages included in the analysis workflow have the status "Complete").

During the "Generate reports" stage, the system considers all report templates that match the above conditions and generates reports for these templates if at least one of the following conditions is met:

  • If the sample analysis workflow includes somatic and/or germline SNVs/Indels discovery, then to generate a report, its template must include at least one block with SNVs/Indels that match the origin with the SNVs/Indels discovered in the sample. Thus, if somatic SNVs/Indels were discovered in a sample, then blocks with somatic SNVs/Indels will be generated. And if germline SNVs/Indels were discovered for a sample, then blocks with germline SNVs/Indels will be generated for a sample.
  • If the sample analysis workflow includes structural variations discovery, then to generate a report, its template must include at least one block with structural variations (in this case, it is mandatory to include SNVs/Indels and/or copy number variations discovery in the sample analysis workflow).
  • If the sample analysis workflow includes copy number variations discovery, then to generate a report, its template must include at least one block with copy number variations.
  • A report whose template includes a block with polygenic traits will be generated for a sample if the following conditions are met:
    1. The sample analysis workflow includes the polygenic risk scores calculation.
    2. The sample analysis workflow includes SNVs/Indels and/or copy number variations discovery.
    3. If QC and imputation are included in the workflow, then the sample must pass the quality control.
  • The report template includes only blocks that are independent of the analysis stages. These are blocks such as "Section", "Patient info", "Sample info", "Control (normal) sample info" (if the samples were uploaded as a tumor/control sample pair), "Formatted text", "Disclaimer", "Sign place", "Clinical trials", "Glioma: Literature".

The "Generate reports" stage completes the sample analysis.