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Compare the effect allele of GWAS SS and UKBB AFib Plink files #14

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jackosullivanoxford opened this issue Jun 17, 2019 · 0 comments

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jackosullivanoxford commented Jun 17, 2019 •

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In step 1 of LDpred, make sure the effect allele in the GWAS Summary Statistics is being entered appropriately into step 1 ldpred code, e.g. --A1 (ldpred code) = Allele1 (GWAS SS), also make sure it matches the PLINK files (which are used as the LD reference panel)
In step 3 of LDpred, make sure the effect allele (A,T, C, G) are the same between the GWAS Summary statistics and the AFib genotype file.

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