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applied to input studies. Setting <code>GENOMICCONTROL ON</code> requests that
applied to input studies. Setting <code>GENOMICCONTROL ON</code> requests that
METAL should automatically calculate and apply an appropriate genomic control
METAL should automatically calculate and apply an appropriate genomic control
correction to each study.
correction to each study. This option can be enabled or disabled for each input
file independently.
Newer versions of METAL also now allow for a specific genomic control parameter
Newer versions of METAL also now allow for a specific genomic control parameter
as input. In this case, instead of automatically calculating the GENOMICCONTROL
as input or for genomic control values to be calculated using a pre-defined marker
value based on available data, METAL will apply the correction according to a
list.
user-specified parameter. This option is convenient when full genome scan results
== Default Usage ==
In the simplest case, genomic control is enabled and Metal automatically calculates and
applies a correction (if appropriate) using all available markers.
Example:
GENOMICCONTROL ON
== User Specified Genomic Control Parameter ==
In this case, instead of automatically calculating the genomic control
value based on available data, METAL will apply a
user-specified correction. This option is convenient when full genome scan results
are not included in METAL input files.
are not included in METAL input files.
GENOMICCONTROL 1.1
GENOMICCONTROL 1.1
== Genomic Control Parameter Calculated Using a Subset of Markers ==
In this case, only a subset of available markers are used to calculate the appropriate
genomic control value. This strategy is useful in fine-mapping experiments where many
markers are expected to show strong evidence for association and should be excluded from
genomic control calculations.
This option is convenient when full genome scan results
are not included in METAL input files.
Example:
GENOMICCONTROL LIST snps.txt
