Difference between revisions of "EIGENSOFT"

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==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR
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* HPC_{{uc:{{#var:app}}}}_DIR
* HPC_{{#uppercase:{{#var:app}}}}_BIN
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* HPC_{{uc:{{#var:app}}}}_BIN
 
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Latest revision as of 21:20, 6 December 2019

Description

eigensoft website  

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