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Update hla_consensus.wdl to handle ambiguity codes. #100

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chrisamiller opened this issue Mar 22, 2023 · 0 comments
Open

Update hla_consensus.wdl to handle ambiguity codes. #100

chrisamiller opened this issue Mar 22, 2023 · 0 comments
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enhancement New feature or request

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@chrisamiller
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Sometimes the clinical reports report HLA codes like "HLA-B*08:YETY" that don't match our expected four digit resolution like HLA-\w*\d{2}:\d{2}

This site contains a list of ambiguity codes and the alleles they match up with. https://hml.nmdp.org/MacUI/

For example, HLA-B*08:YETY translates to three options: HLA-B*08:01/HLA-B*08:19N/HLA-B*08:109

The goal is to update the hla_consensus.wdl code to handle these intelligently by:

  1. disambiguating any codes from the clinical HLA typing inputs
  2. comparing the possibilities to those reported by Optitype or Phlat and choosing the alleles that match
  3. if there is no disambiguation, or there is no match, drop the ambiguous coded allele and handle the rest in the same way as is currently done (unique union?)
@malachig malachig added the enhancement New feature or request label Mar 24, 2023
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