Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

✨ Import coordinates from Sheep and Goat projects #18

Closed
5 tasks done
bunop opened this issue Jul 1, 2021 · 1 comment · Fixed by #90
Closed
5 tasks done

✨ Import coordinates from Sheep and Goat projects #18

bunop opened this issue Jul 1, 2021 · 1 comment · Fixed by #90
Labels
enhancement New feature or request

Comments

@bunop
Copy link
Member

bunop commented Jul 1, 2021

Is your feature request related to a problem? Please describe.
Sheep and Goat projects have SNPs coordinates for the four major assemblies I need (CHI1, ARS, OAR3, OAR4)

Describe the solution you'd like
Check genomic coordinates, make a report and then fill those data into database

Describe alternatives you've considered
Data could be fetched directly from EBI or EnsEMBL, however it's interesting to merge multiple data sources to understand where problems could be. Data from consortium will not be used to provide the final data files, evaluate if these information need to be provided with final version

Additional context
Those data could be useful to cover missing informations (like rs in goat). This data lacks of alignment information, so getting illumina_top from this type of data make no sense.

  • Manage the two different data files provided by consortium
  • Force data update when importing from consortium
  • Track date when importing from consortium
  • Determine illumina_top data directly from variant for Sheep
  • Import data for goat
@bunop bunop added the enhancement New feature or request label Jul 1, 2021
@bunop bunop added this to the SMARTER database v1.0.0 milestone Jul 7, 2021
@bunop
Copy link
Member Author

bunop commented Apr 20, 2023

The latest data available in figshare for sheep consortium track genotypes as ALT/REF, so I cannot manage this genotype at the moment. We need to:

  • manage ALT and REF in Location objects
  • shuffle ALT/REF to determine the illumina SNP and the strand
    or
  • put illumina strand from variation record and then track only ALT and REF

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
Archived in project
Development

Successfully merging a pull request may close this issue.

1 participant