From Genome Analysis Wiki
Jump to navigationJump to search
891 bytes added
, 07:34, 25 March 2011
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 |