Filter view
In case no conclusive diagnosis can be reached based on the results of Moon’s automated filter pipeline, manual filtering of the rare variants in the VCF is required.
As such, negative results from the automated pipeline can be manually confirmed. In addition, variants that are not included in the scope of the automated filter pipeline (eg. genes that have not yet been linked to disease; known genes linked to new disease phenotypes), or that were missed by the automated pipeline can be manually identified and added to the list of results.
Additionally, it is possible to manually analyse samples in Moon without specifying an input phenotype (eg. if phenotype info is not available, or if the analysis is rather preventative). In this case, no automated analysis is possible and manual filtering of the data will be required.
Manual filtering is performed in the Filter view, which can be accessed via the Filter tab on top of the screen.
The Filter view contains two main elements:
The panel on the left shows all filters that can be applied to the variant data. Below the filters on the left, it is indicated how many variants are in accordance with the combination of filter settings chosen and how many of these are already displayed on the right. Clicking the download button next to this allows you to download all matching variants (and their annotations) in a .txt csv file.
A toggle at the top of the screen allows you to switch between the SNV and SV Filter views.
On the right, you see details of the variants that match the combination of all filter criteria you set in the panel on the left.
SNVs can be listed multiple times in the variant list on the right, if they are located within overlapping genes. In this case, the variant will be annotated multiple times, in each overlapping gene.
Moon provides live filtering, meaning that the list of displayed variants is immediately updated upon changing one of the filter criteria on the left.
Filter results are ranked according to phenotype overlap of the annotated disorder and the input phenotype.
For each of the resulting variants, a summary of the most relevant annotations are provided, in addition to more details in the variant card, similar to the annotations shown for variants in the Shortlist. For each variant, it is indicated that the variant has either been shortlisted by the automated pipeline, or why the automated pipeline excluded the variant from the shortlist.
On the right of the variant annotation bar, three icons are displayed:
The left icon allows to add a variant to the Knowledge base (SNV only).
The right icon allows to open the variant card for more detailed annotation.
The star icon in the middle, allows to add or remove a variant that was not shortlisted by Moon, to or from the Shortlist, respectively.
When manually adding variants to the shortlist, these will appear in the ‘Manually filtered’ tab on the Shortlist page. From there, manually added variants can be reported similarly to automatically shortlisted variants.