PEDIA integration into VarFish

[ahujameg]

PEDIA is an approach for prioritization of exome data by facial image analysis.
It would be advantageous to include phenotypic scores such as PEDIA into VarFish. The VarFish users would be able to prioritize the variants based on the the face scores.

We can add another option for PEDIA score (like the Mutation Taster) in pathogenicity scoring method drop-down present in the Prioritization tab in the Filter Variants page.
When the user clicks on 'Filter & Display' button, the variants will be filtered and another column for showing the PEDIA score will be displayed in the results table.

[ahujameg]

Documenting ideas generated with Tzung-Chien:

Options for Output from VarFish:

• Excel sheet separated by comma or tab
• VCF format
• Keep only index

Pre-filtering step:

• Filter out variants in introns, frequent variants (allele frequency more than 5%) -- Confirm on this?

Information we need in the file:

• Chr
• Position
• Ref
• Alt
• Gene symbol
• Allele frequency gnomad, 1KG, ExAC
• CADD Score.

[ahujameg]

About the approach Tzung discussed on 29th March, I think instead of allowing to upload an image though inside VarFish interface, there should be an option like the MutationTaster which takes the user to an external link of PEDIA using which the user uploads the image which then goes into the GMDB.

[ahujameg]

Comments by Alexej:
"also gut idea
i mean, ultimately it should be as easy for the user as possible.
and prior to submission of the large unfiltered VCF file to PEDIA, one would actually need to filter it for once, (in order to remove frequnt variants and apply mode of inheritance filter, and only then, one should be able to send the VCF with HPO terms and picture to pedia

ideally, after hitting the send-to-PEDIA button one would have to login, would get a token, and a new case is created"

[alexschmid-igsb]

My comment while discussing with Meghna: "I think that VarFish is a tool for data analysis rather than data management. Therefore data should be managed somewhere else. The idea to redirect the user to an external page to enter new data for a case (pictures, hpo terms, etc.) is good. It helps to manage the data in a centralized manner. Further, there is more than one source to feed specific data (hpo term, images) into our architecture. It could become complicated to do this in VarFish, it should be done centralized."