PLINK meta-analysis when there is SNP for just one study

Question

[kl]

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

[chrchang523]

What plink build are you using? This should have been fixed in plink 1.9 in December 2017.

[zx8754]

I am guessing, if we do not use report-all, that SNP won't be present in the output file. With report-all option 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.