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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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RS Lims Export file changes #162

Closed LordRust closed 5 months ago

LordRust commented 5 months ago

Adaptations to the export file format for TB variant calling.

Changes:

  1. Parameter fields uses underscore
  2. All variants should follow the Variant column from the WHO catalogue if possible. Regardless of length of the field (yes a reversion from the wishes that we got earlier). And since everything now follows HGVS as far as we can (but we do not add the genome prefix NC_000962.3:). And while we are at it, lets name the Delly results accordingly, since we will be the curators of the data, but for RS lims making a difference in how we found the deletion is mostly just confusing for the physicians.
    • Long ones are OK: rrs_n.1022_1032delTTGTGGCCTGTinsCTTCGGGGGACAAA;whiB7_p.Thr10_Gln13del;lpqB_c.729C>T
    • Delly currently is SV_DEL_79570-83034 --> change to g.79570_83034del
  3. MTBC_QC parameter added. This should be Fail if the sample has a QC status of "Permanent fail"
  4. If MTBC_QC=='Fail' then set all results to the antibiotics to "Ej bedömbart"

MTBC_ART and MTBC_LINEAGE could potentially come out with multiple values. If so, separate the values with semicolon

Example output file

sample_id   parameter   result  variants
test_mtuberculosis_1    RIF_NGS Mutation påvisad    lpqB_c.729C>T WHO-2;g.79570_83034del
test_mtuberculosis_1    INH_NGSH    Mutation ej påvisad 
test_mtuberculosis_1    INH_NGSL    Mutation påvisad    inhA_c.-10_-9insAGG WHO-1
test_mtuberculosis_1    PYR_NGS Mutation ej påvisad 
test_mtuberculosis_1    ETB_NGS Mutation ej påvisad 
test_mtuberculosis_1    AMI_NGS Mutation ej påvisad 
test_mtuberculosis_1    LEV_NGS Mutation ej påvisad 
test_mtuberculosis_1    MTBC_ART    Mycobacterium tuberculosis  
test_mtuberculosis_1    MTBC_LINEAGE    lineage2.2.1    
test_mtuberculosis_1    MTBC_QC Pass