germline vs somatic variants

[nlwashington]

we will need to disambiguate between variants (and perhaps any geno partonomy) that are germline vs somatic.

how should these be represented? should there be classes for "germline variant" "somatic variant", or perhaps there is some kind of property about the origin of the variation "germline origin". if it's a "somatic origin", i could see perhaps linking the origin to a tissue or cell type, if known.

the usecase for this is particularly for cancers, where major changes to the genome (chromosomal rearrangements) happen in only a subset of the cells but not the germline. also, it's possible that we might want to reason differently based on the origin, and in interfaces filtering/sorting on the origin is important.

we hadn't really needed this before as with mice and fish they were generally somatic, but in humans we definitely need it.