Difference between revisions of "EIGENSOFT"
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Revision as of 21:20, 6 December 2019
Description
EIGENSOFT uses PCA to correct for population stratification in medical association studies (EIGENSTRAT, Price et al. 2006) and to detect and analyze population structure (SMARTPCA, Patterson et al. 2006).
Required Modules
Serial
- eigensoft
System Variables
- HPC_EIGENSOFT_DIR
- HPC_EIGENSOFT_BIN
Citation
If you publish research that uses eigensoft you have to cite it as follows:
Price, Alkes L., et al. "Principal components analysis corrects for stratification in genome-wide association studies." Nature genetics 38.8 (2006): 904-909.
and
Patterson, Nick, Alkes L. Price, and David Reich. "Population structure and eigenanalysis." PLoS genetics 2.12 (2006): e190.
Validation
- Validated 4/5/2018