Dashboard

There is a dashboard available in the top left menu. The purpose of this one is to collect statistics of cases/institutes/variants in scout. The default is to show information for the whole instance. A user can also see specific information for the institute/institutes that they can access. We will here describe in more detail what the numbers mean.

Basic statistics

Wgs samples

The number of samples in all cases that have the analysis tag WGS (Whole Genome Sequencing). Note that there will probably be more samples than cases.

Wes samples

The number of samples in all cases that have the analysis tag WES (Whole Exome Sequencing).

All cases

Total number of cases in database

Tagged cases

The rest of the boxes shows how many cases there are with the different statuses and fraction of all. E.g. if all cases = 100 and 10 are archived the fraction will be 10%

Pedigree information

Displays how many cases that there are of different family sizes. Everything with more than 3 individuals is grouped into the 'Many' category.

Cases with...

Some more detailed information about cases.

Phenotype terms

Number of cases that have at least one phenotype term

Similar for the following.

Variants

Validation ordered

Number of variants with validation ordered. This number could be higher that Cases with validation ordered since one case could have multiple variants where validation is ordered.

Validated True Positive

Number of variants that are validated True positive. Fraction is #True positive/(#True positive + #False positive)

Validated False Positive

Similar to the above