Closed priesgo closed 1 year ago
https://covariants.org/variants https://github.com/hodcroftlab/covariants/blob/master/web/data/clusters.json
The data provided by the Covariants team could be another source of lineage-defining mutations. They are divided into synonymous and non-synonymous mutations. The lineages are defined using the Nextstrain classification.
The covariants resource looks better structured. Feel free to use this if it helps you
Done. Closing the issue
Following up on #61 we want here to include in the DB the mutations that are described to conform a given lineage. This is slightly different from the mutations that are observed in the samples from this lineage.
We could create a table
LineageVariant
with one FK pointing to theLineage
table and another FK pointing to theVariant
table.Potential issues:
Variant
table contains the functional annotations coming from SnpEff. This information is obtained from the VCF files that come out of the pipeline. We won't be able to add this information if the database does not contain this variant beforehand.