Variant Types Update

Correcting Hierarchical Queries for Variant Type


The variantType query parameter - recommended only for non-precise variants, i.e. such w/o a specified allele - is now being expanded correctly. In Progenetix these are only CNVs, all expressed as (sub)classes of EFO:0030066 (relative copy number variation):

  EFO:0030066:
    child_terms:
      - EFO:0030066
      - EFO:0030067
      - EFO:0030068
      - EFO:0030069
      - EFO:0030070
      - EFO:0030071
      - EFO:0030072
      - EFO:0030073
  EFO:0030070:
    child_terms:
      - EFO:0030070
      - EFO:0030071
      - EFO:0030072
      - EFO:0030073   
...etc.

The different variantState classe can easily be aliased which e.g. allows vor DUP-style shorthand.

variant_state_aliases:
  CNV: EFO:0030066
  EFO:0030066: EFO:0030066
  DUP: EFO:0030070
  EFO:0030070: EFO:0030070

Therefore, a search w/ a variantType parameter of EFO:0030066 or DUP will now correctly return samples w/ any type of CNV at the indicated location.