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Clinical-Genomics-Lund / bonsai

Visualize and analyze resistance and outbreak of bacterial pathogen
https://bonsai-wgs.readthedocs.io/en/latest/
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Updated LIMS export format #179

Closed mhkc closed 5 months ago

mhkc commented 5 months ago

This PR updates the RS LIMS export format for M. tuberculosis.

Close #162

How to setup and perform the tests

  1. Load a few samples TB into the database
  2. Fail one sample based on QC and set the reason to "permanent fail"
  3. Accept another sample with predicted resistance variants and a DELLY file
  4. Verify a few variants and annotate additional rifampicin or high/ low grade isoniazide resistance

Expected outcome

  1. Output should follow the guidelines in #162
  2. Samples with "permanent fail" QC should be set as "Ej bedömbart"
  3. Variants should only be displayed for the first line drugs
  4. Variants should be described in a HGVS-like nomenclature