Question: METAL (gwas meta-analysis tool)
0
gravatar for bigfoot
8 months ago by
bigfoot10
bigfoot10 wrote:

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!!

ADD COMMENTlink modified 8 months ago • written 8 months ago by bigfoot10

Post the full command.

ADD REPLYlink written 8 months ago by zx87549.7k
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

QUIT
ADD REPLYlink modified 8 months ago • written 8 months ago by bigfoot10
0
gravatar for bigfoot
8 months ago by
bigfoot10
bigfoot10 wrote:

I updated the software, now it works amazingly!

ADD COMMENTlink written 8 months ago by bigfoot10
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