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PharmGKB / PharmCAT

The Pharmacogenomic Clinical Annotation Tool
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No CPIC variants found #158

Closed Bioinf-usr closed 1 year ago

Bioinf-usr commented 1 year ago

Hi,

I am using pharmcat version 2.8.2. In the reported html file, I see that for some of the genes such as CFTR, CACNA1S and RYR1 the inferred genotype is "No CPIC variants found " . May I know what does it mean?

Thank you.

whaleyr commented 1 year ago

It means that no variants that CPIC uses for recommendation lookup were found in the sample data provided for those genes.

Bioinf-usr commented 1 year ago

Sorry, For example in the case of CACNA1S. The variants recommended according to CPIC are c.3257G>A, c.520C>T and Reference. And in my VCF file, I can find them. Even in the report, they are mentioned in the "CACNA1S allele match data" section. Am I missing something? When I look into my VCF file, for these positions there is a custom filter that I have added instead of "PASS". Could that be the reason?

Screenshot 2023-10-12 at 18 39 55
whaleyr commented 1 year ago

More specifically, no variant allele that CPIC uses for recommendations was found. Those two positions are in the sample data but they are both homozygous reference alleles, therefore no variant allele is present.

Bioinf-usr commented 1 year ago

Understood, thank you!!