search

farhat-lab / gentb-site

The genTB project, the Django site, variant calling and prediciton pipeline, and mapping pipeline with hooks to two ravens
https://gentb.hms.harvard.edu
Other
8 stars 11 forks source link

Revise lipworth scheme from predict lineage caller #207

Closed mahafarhat closed 3 years ago

mahafarhat commented 3 years ago

Lipworth snp scheme has errors and currently producing incorrect predictions. Luca can fix this error later (low priority), but he stated that by deleting the lipworth snp data file we can stop generating a prediction automatically using this scheme. Lipworth prediction should be deleted from the site.

mahafarhat commented 3 years ago

Ok I did discuss this with @ejfresch. @ejfresch said we should report the snp counts for lipworth scheme as percentages next to the lineage call itself. it is better to keep the lipworth scheme as it is the only one that has animal lineages and gives families ~ to spoligotyping.

mahafarhat commented 3 years ago

@ejfresch @doctormo can you please work together to resolve this issue by 4/20?

doctormo commented 3 years ago

The Lineage webpage is controlled by the pipeline, whatever appears in that resulting lineage file is what is displayed to the user, no filtering is applied except to shuffle each into the right columns.

@ejfresch Do you know what parts of the lineage caller pipeline program need to be modified to do what Maha wants here?