User Messages - FASTQ and alignment QC

User messages are intended to easily and conveniently alert the user of any quality standard that was not met for the analysis

VarSome Clinical  has introduced a new display to highlight quality issues related to the user input data and ensure that they won't be missed. The easily accessible display consists of badges of different colors based on their severity (errors-red, warnings-amber and information-blue). These messages are visible both on “Dashboard”/'Analyses” and “Variant table” menus, per sample and provide useful information about the status of each sample during the quality control step.

Quality control is performed at the FASTQ (FASTQC tool) and the BAM level, to ensure that the raw data is good enough to reliably analyze the results. For each analysis, warning or error icons may appear on the "Analyses" / "Dashboard" menu to inform the users that the quality control of the FASTQ file produced warnings and/or errors.

To reduce the number of error/warning messages displayed on the “Analyses”/ “Dashboard” menu and improve their practicality, FASTQC errors have been divided into three groups according to their frequency: Frequent, Standard and Rare. The Frequent messages include Per base sequence content as well as Per sequence GC content. Frequent errors will not display any warning or error message, therefore their messages will not appear as warnings or errors on the "Analyses" / "Dashboard" menu. 

On the other hand, Standard errors include:

  • Per tile sequence quality
  • Overrepresented sequences
  • Adapter Content
  • Sequence Duplication Levels

and will display a single warning when there is more than two present in the report. 

Note: Sequence Duplication Levels will be ignored when the analysis used an amplicon kit. 

Finally, Rare errors include:

  • Per base sequence quality
  • Per base N content
  • Per sequence quality scores
  • Sequence Length Distribution

and will display an error message when there is one or more of them present in the report.

To know more about what parameters of FASTQC have risen the flag, you can click on the icons, and a pop-up window will appear showing you a detailed description.

The same information is also available in the variants table for an individual analysis:

In the same way, there are some quality checks run at the alignment level that will produce warnings and/or error messages in case there are issues with the coverage of the sample. Additionally, if one sample included in a CNV cohort analysis does not have enough coverage, the whole CNV analysis will fail and an error message will be displayed informing about the problematic sample.