PharmCAT returning rsid for diplotype calls in SLCO1B1

[anh151]

• Do you want to request a feature or report a bug? Bug

• What is the current behavior? This behavior has only occurred for SLCO1B1. For some samples PharmCAT returns some variation of rs4149056T/rs4149056T, rs4149056C/rs4149056T, or rs4149056C/rs4149056C as the diplotype call.

• If the current behavior is a bug, please provide the steps to reproduce and, if possible, your example input data via a Gist or similar. Consider a sample with the following variants for SLCO1B1. This VCF represents the output from the preprocessor.

CHROM | POS | REF | ALT | 123456

-- | -- | -- | -- | -- chr12 | 21176804 | A | G | 1/1:.:69:157 chr12 | 21178615 | T | C | 1/1:.:99:213 chr12 | 21239042 | A | C | 0/1:.:48:85

Summarized json output below: {'diplotypes': ['rs4149056C/rs4149056C'], 'gene': 'SLCO1B1', 'variantsOfInterestUnspecified': True, 'outsideCall': False, 'totalMissingVariants': 1, 'totalVariants': 31, .... 'phaseStatus': 'Unphased', 'extra-position-notes': [], 'uncalledHaps': '*45', 'hasUncalledHaps': True, 'messages': [], 'unphased': True}

{'gene': 'SLCO1B1', 'chromosome': 'chr12', 'position': 21239042, 'dbSnpId': 'rs34671512', 'call': 'A/C', 'alleles': ['19', '20', '40'], 'phased': False, 'wildtypeAllele': 'A', 'mismatch': False, 'warnings': []} {'gene': 'SLCO1B1', 'chromosome': 'chr12', 'position': 21176804, 'dbSnpId': 'rs2306283', 'call': 'G|G', 'alleles': ['14', '15', '20', '24', '25', '27', '28', '29', '30', '31', '32', '33', '37', '39', '42', '43', '44', '46', '47'], 'phased': True, 'wildtypeAllele': 'A', 'mismatch': False, 'warnings': []} {'gene': 'SLCO1B1', 'chromosome': 'chr12', 'position': 21178615, 'dbSnpId': 'rs4149056', 'call': 'C|C', 'alleles': ['5', '15', '40', '46', '*47'], 'phased': True, 'wildtypeAllele': 'T', 'mismatch': False, 'warnings': []}

Expected diplotype here would be Indeterminate/Indeterminate which might be reported as "not called" by PharmCAT since this sample has 3 possibilities that all contain 3 alleles (15/15/19;15/37/40;5/15/*20)

• Please tell us about your environment:

  • PharmCAT Version: 1.8.0
  • JDK Version: jdk-14.0.2+12
  • Environment: Linux

Hope this helps. I can provide more examples if needed. This affects ~0.2% of samples.

Andrew

[whaleyr]

This is expected behavior and is documented on our Gene Definition Exceptions page.