Support for multi-variants across multiple sequences

[afrubin]

To support the definition of multiple target sequences for a single MaveDB score set, mavehgvs will need to support multi-variants across multiple target sequences.

The nomenclature for doing this is defined in HGVS:

I have a patient with hearing loss and variants in the GJB2 (c.35delG) and GJB6 (c.689_690insT) genes, how should I describe this? (Nancy Carson, Ottawa, Canada)

The recommendation is to use the format GJB2:c.[35delG] GJB6:c.[689_690insT]. This uses standard HGVS descriptions and prevents confusion regarding which variant was found in which gene. Note it is essential that you also define the coding DNA reference sequence used. Another format, coping with this directly, is to describe the variants as NM_004004.2:c.[35delG] NM_006783.1:c.[689_690insT], i.e. using the Genbank reference sequences in stead of the HGNC approved Gene Symbol.

Related tasks:

• [ ] Add test cases for multi-target multi-variants, including invalid variants that lack the [] around the individual parts.
• [ ] Update patterns to support the new syntax.
• [ ] Add dictionary support for this type of multi-variant.
• [ ] Update specification in the documentation to include a new section on multi-variants (including single-sequence multi-variants with or without an identifier).

[bencap]

Note that right now although multi variants would be validated by our biocommons HGVS parser, their prefixes are not validated properly by our internal library code.