Cross database links - labsquare/cutevariant GitHub Wiki

Purpose

There are many different databases of variants, so we wanted to let the user selects its favorite one. By setting this parameter, you will be sent directly to the page of a variant on a given database.

Create your first mask

First go to: File > Settings > "Variant view" tab. Click on Add, give a new to your mask Then the principle is to enter an URL corresponding to the wanted database, including placeholders. Any column of your VCF can be a placeholder. Here are some examples of valid placeholders: {pos}, {ref} or again {rsid} Eventually, click on Save all

Default mask

The default mask controls the database linked with the action of double-clicking on a variant from the variant view. To do that, select an already added mask and click the Set as default button. Your mask should now have a bold font.

Execute a non-default mask

A part from the default mask that is executed by double-clicking, the rest of your (non-default) masks can be executed via the contextual menu of Cutevariant: => Right-click on a variant, then go on 'External links' and click on the name of one of your other masks

Some examples of URL

• For MyVariant.info (mostly hg19): http://myvariant.info/v1/variant/chr{chr}:{pos}{ref}>{alt}
• For IGV (requieres to have an instance of IGV already opened): http://localhost:60151/goto?locus={chr}:{pos}
• For dbSNP: https://www.ncbi.nlm.nih.gov/snp/rsid
• For ClinVar: https://www.ncbi.nlm.nih.gov/clinvar/variation/{clinvar_rs}