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

✨ track ALT and REF alleles in locations #91

Open
2 tasks
bunop opened this issue Apr 20, 2023 · 0 comments
Open
2 tasks

✨ track ALT and REF alleles in locations #91

bunop opened this issue Apr 20, 2023 · 0 comments
Labels
enhancement New feature or request

Comments

@bunop
Copy link
Member

bunop commented Apr 20, 2023

Is your feature request related to a problem? Please describe.
Tracking ALT and REF alleles for each location is required to convert data into VCF format

Describe the solution you'd like
ALT and REF alleles should be determine from genome alignments and then tracked for each Location object

Describe alternatives you've considered
The sheep genome consortium tracks genotypes with REF/ALT convention, data can be imported from here. However, all the SNPs not managed by them (ie Affymetrix) cannot have these attributes

Additional context
Please see comments in #18 for import_consortium.py

  • Add ALT and REF class attributes to src.features.smarterdb.Location
  • Track latest data from Sheep genome consortium
@bunop bunop added the enhancement New feature or request label Apr 20, 2023
@bunop bunop added this to the SMARTER database v1.0.0 milestone Apr 20, 2023
@bunop bunop added this to SMARTER Aug 3, 2023
@bunop bunop moved this to To do in SMARTER Aug 3, 2023
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
Status: To do
Development

No branches or pull requests

1 participant