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本篇,介绍GCTA这个软件的安装。
GCTA官网:https://yanglab.westlake.edu.cn/software/gcta/#Download
这个软件是开源的,源码在github上:https://github.com/jianyangqt/gcta
在终端中运行下面命令:
wget https://yanglab.westlake.edu.cn/software/gcta/bin/gcta_1.94.0beta.zip
下载成功:文件:
gcta_1.94.0beta.zip
unzip gcta_1.94.0beta.zip
文件:
gcta_1.94.0beta ├── gcta64 ├── MIT_License.txt ├── README.txt ├── test.bed ├── test.bim ├── test.fam └── test.phen
进入gcta_1.94.0beta
文件夹,运行下面命令:
根据plink的二进制文件,进行G矩阵的构建(Yang的方法),生成二进制亲缘关系矩阵。
./gcta64 --bfile test --make-grm --out gmat
运行日志:
Options: --bfile test --make-grm --out gmat Note: GRM is computed using the SNPs on the autosomes. Reading PLINK FAM file from [test.fam]... 3925 individuals to be included from FAM file. 3925 individuals to be included. 1643 males, 2282 females, 0 unknown. Reading PLINK BIM file from [test.bim]... 1000 SNPs to be included from BIM file(s). Computing the genetic relationship matrix (GRM) v2 ... Subset 1/1, no. subject 1-3925 3925 samples, 1000 markers, 7704775 GRM elements IDs for the GRM file have been saved in the file [gmat.grm.id] Computing GRM... 100% finished in 0.3 sec 1000 SNPs have been processed. Used 1000 valid SNPs. The GRM computation is completed. Saving GRM... GRM has been saved in the file [gmat.grm.bin] Number of SNPs in each pair of individuals has been saved in the file [gmat.grm.N.bin]
结果文件:
gmat.grm.bin gmat.grm.id gmat.grm.N.bin gmat.log
在bin中打开git终端:
运行代码:
./gcta64.exe --bfile ../test --make-grm --out ../gmat
结果文件:
可以看到,Windows和Linux运行命令一致。gcta也有Mac系统,和plink类似。
为了使用更方便,可以将gcta64可执行文件放到bin文件下,这样就可以直接键入gcta64进行分析。
「windows下:」
cp gcta64.exe ~/bin/
「Linux下:」
cp gcta64 ~/bin/
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