What is the best way to label loss-of-function variants to then perform GWAS on LoF variants and phenotypic outcome? Would a SnpEff -> SnpFilt -> Plink2 pipeline make sense? I am new to this type of research! Permanently deleted user 28 April 2022 00:00 2 comments Comments 2 comments Sort by Date Votes Ondrej Klempir DNAnexus Team 02 May 2022 08:06 UKB RAP documention provides this page, see https://dnanexus.gitbook.io/uk-biobank-rap/science-corner/using-regenie-to-generate-variant-masks 0 Ondrej Klempir DNAnexus Team 02 May 2022 08:07 an example of GWAS and phenotypic outcome is then here: https://dnanexus.gitbook.io/uk-biobank-rap/science-corner/gwas-ex 0 Please sign in to leave a comment.
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UKB RAP documention provides this page, see https://dnanexus.gitbook.io/uk-biobank-rap/science-corner/using-regenie-to-generate-variant-masks
an example of GWAS and phenotypic outcome is then here: https://dnanexus.gitbook.io/uk-biobank-rap/science-corner/gwas-ex
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