PLINK meta-analysis when there is SNP for just one study
Hi,
I am encountering an issue with my meta-analysis. Although, plink reads all 3 studies, when there is 1 study it outputs NA for the betas, SEs and associated values even though I specify for it to report all
--meta-analysis SP_reformatted.assoc GC_reformatted.assoc AP_reformatted.assoc + qt report-all
Would really appreciate advice
Thanks
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I am guessing, if we do not use
report-all, that SNP won't be present in the output file. Withreport-alloption we are saying list the SNP even if there is no stat, hence NA.I prefer METAL for meta analysis, which reports for all SNPs even if that SNP only present in one study.
What plink build are you using? This should have been fixed in plink 1.9 in December 2017.