Quality Control Report

In order to find the Quality Control (QC) Report of an analysis in VarSome Clinical you can go either: 

  1. to the Samples page and select from the burger menu of the analysis you wish the "View QC Report" or
  2. in the Variant Table page you can click on the "Analysis actions" button and select the same option.

 

Quality Control report for germline/somatic analyses

A QC report includes all of the categories presented below:

General information

Simple information about the user, the reference genome, the sequencing technology, the file name and the type of pipeline used.

Software and Database versions

Information about Saphetor's and Sentieon's software versions used for alignment and variant calling and all available sources' versions that were used in the pipeline for annotation.

Read alignment results

This matrix reports information about the alignment of all reads and on the targeted regions of the selected assay.

Regions reported and Average region coverage

Display of information regarding the assay used for the analysis and the average coverage of the targeted regions.

Coverage

This matrix shows the coverage depths and percentages of all positions in total and of the targeted regions

Number of identified variants by class

The matrix presents the number of automatically classified variants in each of the 5 standard  pathogenicity classes.

Summary for ACMG Rules

Display of the number of times (and its percentage) each ACMG rule was triggered.

Number of SNV found in coding regions

 

Quality Control report for CNV analyses

The QC report of a CNV analysis can be accessed following these steps:


  • CNV analysis table: 
    • Sample name.
    • Coverage (median): median coverage across all target regions of the sample.
    • Number of reference samples: number of samples used to construct the reference set of samples.
    • Reference sample names: sample names belonging to the reference set.
    • Correlation: correlation coefficient between the test and its reference set of samples.
    • Gender (predicted): gender prediction automatically performed by the pipeline.
    • Sex (user defined): gender defined by the user (only for samples analyzed with the somatic pipeline).
    • wsex (consensus): sex of the samples in the cohort.

If the samples of the cohort are of not of the same sex or if their sex is not known, the CNV calls obtained for chromosomes X and Y will not be reliable and VarSome Clinical will not display them.