Difference between revisions of "GCTA"

From UFRC
Jump to navigation Jump to search
m (Text replacement - "#uppercase" to "uc")
 
(One intermediate revision by the same user not shown)
Line 1: Line 1:
[[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:SNP]]
+
[[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:Variant Calling]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|gcta}}
 
|{{#vardefine:app|gcta}}
Line 21: Line 21:
  
 
<!--Modules-->
 
<!--Modules-->
==Required Modules==
+
==Environment Modules==
 
+
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
===Serial===
 
* {{#var:app}}
 
<!--
 
===Parallel (OpenMP)===
 
* intel
 
* {{#var:app}}
 
===Parallel (MPI)===
 
* intel
 
* openmpi
 
* {{#var:app}}
 
-->
 
 
==System Variables==
 
==System Variables==
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
Line 78: Line 67:
 
<!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
 
<!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
 
__NOTOC____NOEDITSECTION__
 
__NOTOC____NOEDITSECTION__
=Validation=
 
* Validate 4/5/2018
 

Latest revision as of 12:56, 15 August 2022

Description

gcta website  

GCTA (Genome-wide Complex Trait Analysis) was originally designed to estimate the proportion of phenotypic variance explained by genome- or chromosome-wide SNPs for complex traits (the GREML method), and has subsequently extended for many other analyses to better understand the genetic architecture of complex traits.

Environment Modules

Run module spider gcta to find out what environment modules are available for this application.

System Variables

  • HPC_GCTA_DIR - installation directory




Citation

If you publish research that uses gcta you have to cite it as follows:

Yang J, Lee SH, Goddard ME and Visscher PM. GCTA: a tool for Genome-wide Complex Trait Analysis. Am J Hum Genet. 2011 Jan 88(1): 76-82. PubMed ID: 21167468

Full list of citations covering the methods used by the software is available from the project website.