Allow integration of repeat expansions

[holtgrewe]

Is your feature request related to a problem? Please describe. We currently cannot properly include repeat expansion, e.g., as called by expansion hunter.

Describe the solution you'd like Integrate expansion hunter output files.

Describe alternatives you've considered N/A

Additional context

• we need to decide how to properly encode this as small variants

[xiamaz]

Some comments regarding repeat expansion formats:

https://github.com/Illumina/ExpansionHunter/blob/master/docs/06_OutputVcfFiles.md

Example repeat expansion output by expansionhunter:

The genotype field might be almost unusable and we will need to somehow convey the information for the number of repeats contained. Some issues:

The range of repeats considered normal can vary greatly. Should this kind of information be stored somewhere? Expansionhunter results are already being transferred for CADS and it would be very useful to integrate it in some manner.

[xiamaz]

A good database for info on repeats is stripy: https://stripy.org/database

Still need to check their data usage permissions.