METAL (gwas meta-analysis tool)
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21 months ago
bigfoot ▴ 10

Hi everybody

I'm using METAL (version released on 2011-03-25) to perform a meta-analysis between several GWASs (genome-wide association studies). The included GWASs contain partly overlapping samples. I'm trying to correct for this source of bias by utilising the code suggested by the programmers "OVERLAP ON".

But, in the log file, I realized that the code OVERLAP ON is not recognized by the software.

## ERROR: The command you issued could not be processed ...

How could I deal with this issue?

I hope that you can help me.

Many thanks in advance!!

gwas meta-analysis genomics bioinformatics metal • 1.1k views
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Post the full command.

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GENOMICCONTROL ON
SCHEME SAMPLESIZE
OVERLAP ON

# trait1
MARKER SNP
ALLELE A1 A2
EFFECT log(OR)
PVALUE P 
WEIGHT DONTUSECOLUMN
DEFAULTWEIGHT 53293
PROCESS /nfs/home4/polpett/summary_statistics/trait1_eur_jun2017

# trait2
MARKER SNP
ALLELE A1 A2
EFFECT log(OR)
PVALUE P 
WEIGHT Neff
PROCESS /nfs/home4/polpett/summary_statistics/trait2_mds7a_0416a

OUTFILE METAANALYSIS_inputfile1-2_ .tbl
ANALYZE HETEROGENEITY

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21 months ago
bigfoot ▴ 10

I updated the software, now it works amazingly!

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