1， generate whole kinship matrix

/opt/TASSEL5/run_pipeline.pl -Xmx20g

-h *.hmp  

-KinshipPlugin -method Centered_IBS -endPlugin

-export whole.txt -exportType SqrMatrix

2, Creat subset and rest matrix

/opt/TASSEL5/run_pipeline.pl -Xmx20g -forkSubset -h *.hmp  

-FilterSiteBuilderPlugin -bedFile *.bed -endPlugin

-KinshipPlugin -method Centered_IBS -endPlugin

-forkRest -SubtractDistanceMatrixPlugin -wholeMatrix whole.txt -endPlugin

-inputSubset -export rest.txt -exportType SqrMatrixBin

-forkExport -export subset.txt -exportType SqrMatrixBin -inputSubset

3, generate a file containing Kinship files list.

/share/bioinfo/miaochenyong/GWAS/testVCAP/debugVCAP/LinList.txt

只写文件的basename， 不含.grm

/share/bioinfo/miaochenyong/GWAS/testVCAP/debugVCAP/subset
/share/bioinfo/miaochenyong/GWAS/testVCAP/debugVCAP/rest

4， generate phenotype file with PLINK format

/share/bioinfo/miaochenyong/GWAS/testVCAP/debugVCAP/GUI1000.pheno

5, run LDAK

../ldak.4.9 --reml test --mgrm LinList.txt --pheno GUI1000.pheno --kinship-details NO

--reml 指定输出文件basename

--mgrm 指定kinship list 文件位置

--pheno 指定phenotype

重要结果：

.reml

contains the estimates of variance explained (with SDs) for each kinship matrix, as well as estimates of the fixed effects (if no covariates are provided, the only fixed effect will be the intercept). This is the most relevant output file.

example:

Kins:2 Regions:0
Blupfile: test.indi.blp
Regfile: none
Total Samples: 916
With_Phenotypes: 916
Null_Likelihood: -1617.453003
Alt_Likelihood: -1422.400513
LRT_Stat: 390.1050
LRT_P: 1.0000e-16
Component Heritability SD
Her_K1 0.221281 0.051276
Her_K2 0.095329 0.038779
Intercept 19.2178 0.0330

UNL

Chenyong

cmiao@huskers.unl.edu

VCAP