Difference between revisions of "METAL GENOMICCONTROL"

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(Created page with 'The '''GENOMICCONTROL''' setting defaults to off, which means that no correction is applied to input studies. Setting <code>GENOMICCONTROL ON</code> requests that METAL should a…')
 
 
Line 2: Line 2:
 
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.
  
Line 13: Line 28:
  
 
     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

Latest revision as of 07:34, 25 March 2011

The GENOMICCONTROL setting defaults to off, which means that no correction is applied to input studies. Setting GENOMICCONTROL ON requests that METAL should automatically calculate and apply an appropriate genomic control 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 as input or for genomic control values to be calculated using a pre-defined marker list.

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.

Example:

   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