Alex H. Wagner, PhD

This seems like a great topic for GA4GH VRS/VCF alignment. While VRS currently handles this with [Repeated Sequence Expressions](https://vrs.ga4gh.org/en/stable/terms_and_model.html#repeatedsequenceexpression), there is an open issue about how to represent [compound repeated...

We have opted for the `ComposedSequenceExpression` concept in VRS, which is currently in a community PR review stage: https://github.com/ga4gh/vrs/pull/376. I am in favor of aligning Alleles using `ComposedSequenceExpression` to follow...

In addition to the above comments (thank you all!) I have two additional issues with this model, and how it would be used in VRS, that need to be addressed...

> > However, leaving it as non-identifiable (as it currently is) means that the `Genotype.members` array will not be sorted during serialization (but it should be). > > @ahwagner I'm...

> > Taking this approach is viable, but would also require us to add explicit indices for ComposedSequenceExpressions and other `array` structures where order is meaningful. @reece and @andreasprlic do...

Thanks Larry. I think the docs need another round of cleanup to address this and other issues you have raised. Hopefully our work in a single source-of-truth (SOT) document from...

In discussing further with @larrybabb, we believe it is more correct to not translate between expression types. In the case of a RepeatedSequenceExpression, normalization should refine the SequenceLocation to the...

Yes, understood re:GRCh*. We would still need to allow ambiguity codes here and wherever else they are used, but recommend against doing so for variation, specifically. The real problem to...

Today @larrybabb and I discussed this issue and decided that–for now–we have no plans to add RelativeCopyNumber support to VRS v1, and leave this as a v2+ feature.

This decision was reversed in conversation with @larrybabb and @andreasprlic on 10/6.