Annotate lineages with described mutations

[priesgo]

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 the Lineage table and another FK pointing to the Variant table.

• [x] Find an appropriate resource that describes the mutations in each lineage
• [x] Define an appropriate data model (the same variant may occur in multiple lineages...)
• [x] Parse the mutation representation
• [x] Load the data in the DB at startup time

Potential issues:

• Are indels represented in a normal form compatible with what we use in CoVigator?
• MNVs may not be reported together, we may need to merge them
• The 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.

[johausmann]

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.

[priesgo]

The covariants resource looks better structured. Feel free to use this if it helps you

[johausmann]

Done. Closing the issue