Genetic correlation (genetic correlation) of complex traits/features (Complex Trait) calculated using GCTA tools

Gcta, described in the article "Genome-wide Complex Trait Analysis (GCTA)-genome-wide complexity profiling", is an analytical tool based on the development of Genome-wide association analysis, in addition to calculating genetic correlations between different traits/phenotype (traits) , you can also calculate the relationship, the near-cross coefficient ..., the following is a brief introduction to the use of gcta to calculate the genetic correlation of different traits/phenotype.

One, install the Gcta tool on Linux:

Wget-r-np-pk-nh-p./to/your/path/way/gcta Http://cnsgenomics.com/software/gcta/gcta_1.26.0.zip # Download the Gcta tool under Linux unzip Gcta_1.26.0.zip #解压GCTA工具

Two, prepare the plink binary format file, such as test.fam test.bim and  test.bed  

Third, generate test. Grm.bin, test. grm. N.bin and test. Grm.id Format Files

/gcta/gcta64--bfile test--autosome--make-grm--out test #生成grm格式文件 to facilitate genetic correlation analysis at the back

Prepare character/phenotype file, suffix. txt format, do not need title, first column family ID, second column individual ID third and fourth columns phenotypes, similar to plink table file format

V. Calculation of genetic correlations

Gcta/gcta64--reml-bivar--reml-bivar-nocove--grm test--pheno pheno.txt--reml-bivar-lrt-rg 0--out Test

Get files in TEST.HSQ format

The contents of the TEST.HSP file are as follows:

source Variance SE
V (G) _tr1 0.479647 0.179078   #trait 1 Genetic variance and standard error
V (g) _tr2 0.286330 0.181329   #trait 2 genetic variance and standard error
C (g) _tr12 0.230828 0.147958   #trait 1 and 2 Genetic Association Variance and standard error
v (e) _tr1 0.524264 0.176650   #trait 1 residual variance and standard error
V (e) _tr2 0.734654 0.181146   #trait 2 residual variance and standard error
C (e) _tr12 0.404298 0.146863   #trait 1 and 2 residual covariance and standard error
VP_TR1 1.003911 0.033202
vp_tr2 1.020984 0.033800
V (g)/vp_tr1 0.477779 0.176457
V (g)/vp_tr2 0.280445 0.176928
Span style= "Background-color: #ffff00" >rg 0.622864 0.217458  # genetic correlation and standard error
N 3669  # Sample amount

Wherein, RG is the genetic correlation we want, 0.622864 and 0.217458 represent two traits/phenotype between genetic correlation (genetic correlation) and standard error (stand error)

Using the Gcta tool to calculate the genetic correlation of complexity traits (complextrait) (geneticcorrelation)