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→How to define PGx alleles for next generation sequencing
*But whenever we have additional variants, no PGx alleles will be reported
(Note that in practice PharmCAT lets the user decide which allele definitions to use in their [https://github.com/PharmGKB/PharmCAT/wiki/NamedAlleleMatcher-101 NamedAlleleMatcher])
===The Aldy method===
The Aldy method is similar to the PharmCAT method, but with some important notes
- The method takes into account the copy number of each variant
- The method introduces additional PGx variants in order to avoid no-calls. The additional variants have been interpreted and curated by the Aldy team.
- The method uses BAM-files instad of VCF files.
===Which definition should we stick to?===
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