Currently combine_scorefiles will include complex variants (CNVs, HLA, APOE, etc) but they will fail matching. We should perhaps add a flag to this script that drops scores with:
variants that can't be represented in matching (e.g. is_haplotypeis_diplotype)
variants that have an non-null inclusion_criteria columns
as these scores are unlikely to be faithfully calculated within pgsc_calc. Perhaps we should also tabulate variant missingness as a % of sum(weights) missing in addition to % of variants.
Currently
combine_scorefileswill include complex variants (CNVs, HLA, APOE, etc) but they will fail matching. We should perhaps add a flag to this script that drops scores with:is_haplotypeis_diplotype)inclusion_criteriacolumnsas these scores are unlikely to be faithfully calculated within pgsc_calc. Perhaps we should also tabulate variant missingness as a % of sum(weights) missing in addition to % of variants.