Objective
Develop a web app to extract data from GDM, preprocess it, and generate a Flapjack project file that will be used in a Flapjack application for pedigree verification.
Success metrics
| Goal | Metric |
|---|---|
| web page that connects to GDM through BrAPI | |
| Allow users to extract studies (experiment + dataset) | |
| Filter dataset by call rates | |
| perform consensus calling | |
| split dataset into populations based on a selected criteria | |
| generate and download Flapjack project file |
Requirements
| # | Requirement | User Story | Importance | Jira Issue | Notes |
|---|---|---|---|---|---|
| 1 | PedVer: Web-based Application | As a GDM user, I want a webpage that connects to GDM through BrAPI Provide BrAPI links and login credentials for GDM (UI has a dropdown to choose a Study) | HIGH | ||
| 2 | PedVer: Extract Studies | As a GDM user, I want to extract Studies (experiment + Dataset) preview of the data + information on the Study include a property response for dnarun which should have all the germplasm and dnasample metadata and their properties associated with the list of dnaruns provided include a property response field for variants which should have all the marker metadata and their properties | |||
| 3 | PedVer: Filter | As a GDM user, I want to be able to filter data by call rates, either sample call rate or marker call rate | |||
| 4 | PedVer: Consensus | As a GDM user, I want to perform consensus calling | |||
| 5 | PedVer: Split Data | As a GDM user, I want to be albe to split datasets into populations based on selected criteria | |||
| 6 | PedVer: Extract FJ Project File | As a GDM user, I want to generate and download a flapjack project file |
User interaction and design
Open Questions
| Question | Answer | Date Answered |
|---|---|---|