NIMPRESS performs imputation of variants not in patient VCF

[Emilie Wilkie]

Used the 11 loci from Vijayakrishnan_Houlston_2018_NatCom publication as individual inputs for NIMPRESS and PLINK. Only 6 of those are observed in the patient VCF file. PLINK only produces a score output for those 6. However NIMPRESS also produces scores for the other 5 variants. Those variants are on different chromosomes, different locations, different Ref,ALT, Risk alleles, so no pattern. For the 6 individual loci that are in the patient data, NIMPRESS and PLINK produce the same results. When using multiple loci for a composite PRS score, NIMPRESS and PLINK produce similar scores sometimes and other times they differ substantially. Current tests indicate that NIMPRESS performs imputation by using "related" variants.