Question: PLINK meta-analysis when there is SNP for just one study
0
gravatar for rkl
5 days ago by
rkl0
rkl0 wrote:

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

plink • 64 views
ADD COMMENTlink modified 5 days ago by zx87546.2k • written 5 days ago by rkl0
1

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

ADD REPLYlink written 4 days ago by chrchang5234.3k

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.

ADD REPLYlink modified 5 days ago • written 5 days ago by zx87546.2k
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