I currently find myself in a bit of a struggle with applying the GENOMICCONTROL flag.
It is stated in official wiki: "To apply genomic control to the meta-analysis results, just perform an initial meta-analysis and then load the initial set of results into METAL to get final, genomic control adjusted results."
And further also "This option can be enabled or disabled for each input file independently."
However, I cannot seem to enable the GENOMICCONTROL flag at the point of writing out the meta-analysis.
My code looks like this:
# Metal Options
#GENOMICCONTROL ON
AVERAGEFREQ ON
MINMAXFREQ ON
SCHEME STDERR
WEIGHT N
TRACKPOSITIONS ON
#CUSTOMVARIABLE TotalSampleSize
#LABEL TotalSampleSize as N
#Input columns
CHROMOSOME CHR
POSITION POS
MARKER cptid
WEIGHT N
ALLELE EFFECT_ALLELE OTHER_ALLELE
FREQ FREQ_A1
EFFECT BETA
STDERR SE
PVAL PVAL
SEPARATOR TAB
LABEL N AS N
GENOMICCONTROL OFF
PROCESS /home/EasyQC/clean.ukbb_easyQC_ready.gz
CHROMOSOME CHR
POSITION POS
MARKER cptid
WEIGHT N
ALLELE EFFECT_ALLELE OTHER_ALLELE
FREQ FREQ_A1
EFFECT BETA
STDERR SE
PVAL PVAL
SEPARATOR TAB
LABEL N AS N
GENOMICCONTROL OFF
PROCESS /home/clean.fin_v7_easyQC_ready.gz
GENOMICCONTROL ON
ANALYZE HETEROGENEITY
Can anyone let me in on how to apply the GENOMICCONTROL on the meta-analysis results?
Thanks a lot
Hello to everyone
I currently find myself in a bit of a struggle with applying the GENOMICCONTROL flag. It is stated in official wiki: "To apply genomic control to the meta-analysis results, just perform an initial meta-analysis and then load the initial set of results into METAL to get final, genomic control adjusted results." And further also "This option can be enabled or disabled for each input file independently."
However, I cannot seem to enable the GENOMICCONTROL flag at the point of writing out the meta-analysis. My code looks like this:
Can anyone let me in on how to apply the GENOMICCONTROL on the meta-analysis results? Thanks a lot
Soren