Currently, the genotype call is interpreted from the GT field, which is not always reflective of the PL field. GT is determined somewhat based on Hardy-Weinburg, which does not apply to our populations.
Though this is the ideal approach for our own group, I can't help but wonder about other prospective users of the loader. Is using PL a generic approach? Or will other groups want to load genotypes solely based on GT? Should we make it an option?
Currently, the genotype call is interpreted from the GT field, which is not always reflective of the PL field. GT is determined somewhat based on Hardy-Weinburg, which does not apply to our populations.
Though this is the ideal approach for our own group, I can't help but wonder about other prospective users of the loader. Is using PL a generic approach? Or will other groups want to load genotypes solely based on GT? Should we make it an option?