To import results from a VEP, SHSP, or Veridical run click on the "Export all variants" button on your results page. For ASSEDA click on the "Export to CUVD" button. You will receive a notification once all of the results have been imported.
Analyses are MutationForecaster computational runs, such as ASSEDA, SHSP, Veridical or VEP. After importing results from MutationForecaster, select the analysis from the "View All Analyses" page to view its variants and individuals.
Results from different computational analyses are combined in a given variant only if that variant has been given same Individual identifier before importing the analysis results. A "Patient identifier" should be manually inputted before running the MutationForecaster analysis on your variants, unless you have entered patient identifiers into the ID field of your vcf file. If no Patient identifier is given a timestamp will be used and results from different analyses will not be combined.
To view all variants found for an individual, and all analyses performed on this individual, select it from a list of all individuals.
Variant columns can be hidden by clicking the "View/Hide Columns" button on the variant list page. Check the name of the column to hide a particular column or hide all columns from a particular computational tool by clicking a button on the top. Your hidden column preferences will persist throughout your login session, and be used in other pages throughout CUVD, but can be changed at any time.
To filter your results by a certain search criteria, enter the search term in the box beneath the column name and press the Enter key. Numerical fields can take arguments with operands such as ">" and "<". All fields can take the operand "!" to denote a negation of the term. Columns can be sorted by selecting the up or down arrow next to the column name. In cases where a list of values is present in a cell, sorting is based on the first value in the list.
Variants are mapped to genes gradually after they are imported into CUVD. This is a process that occurs in the background. You can map variants immediately by going to the variant’s entry page and clicking "Map now".
Mapping progress is shown in the blue circle in the bottom right corner of CUVD pages.
To search for multiple variants in external databases at once select variants from the list of variants, then select "Search in External Databases" from the table’s option menu reached by hovering over the gear icon above the checkboxes. The search will run in the background and you will receive a notification once the search has been completed.
Performing an external search on a variant searches for the variant in dbSNP, ClinVar, Exome Variant Server (EVS), publically available Leiden Open Variant Databases (LOVD), and PubMed.
PubMed articles are identified if the variant’s ClinVar or dbSNP entry is found under "Related information" on the article’s PubMed entry page. CytoVa is not used in this procedure.
Entries will not need to be edited for normal use of CUVD. There may be some situations where you will wish to modify your data directly.
A variant entry can be edited by clicking "Edit variant entry" from the Options menu on the variant’s page.
Reference: filled in with links to dbSNP, GenBank, or OMIM.
Frequency: Frequency in which the variant was found; e.g 5/760 chromosomes (in 5 of 760 chromosomes tested), 1/33 patients (in 1 of 33 patients analysed in study), 0.05 controls (in 5% of control cases tested). Preferred format is 3/75, not 0.04.
An Individual can be edited by clicking "Edit individual entry" from the Options menu on the variant’s page.
Reference: References to relevant articles using the pubmed id or the DOI.
Investigator: if a particular person from the lab is responsible for investigating data related to this individual put this person’s name here.
Panel size: How many individuals this entry represents
Diseases: configure a disease to add a disease besides "Healthy/Control".
Select the entries you would like to delete by checking the checkboxes, and then click "Delete selected entries" from the options menu.
If deleting a group of variants results in having an Individual with no variants, that Individual will also be deleted. If deleting a group of variants results in having an Analysis with no variants, that Analysis will also be deleted.
Deleting a gene also deletes all variants mapped to that gene.
Deleting a transcript also deletes all variants mapped to that transcript.
Deleting an individual also deletes all variants in that individual.
Deleting an analysis will result in having results from that analysis deleted from its variants. If the variant has been analyzed using another tool those results will remain, but if the variant has not been analyzed using another tool that variant will be deleted.
To download results select "Download all variants" from the option menu. If you wish to only download certain variants, select the variants by checking their checkboxes and click "Download selected variants". To download variants from a specific analysis visit that analysis’ page, "select all variants" from the list of Variants found. In cases where a single variant affects multiple splice sites, results for that variant are given as a list that can be thought of as a subtable. Results are also presented this way when a variant is associated with more than one Ensembl feature.