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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.
The text was updated successfully, but these errors were encountered:
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.
The text was updated successfully, but these errors were encountered: