使用plink、gemma软件进行gwas分析增加协变量
作者：互联网
001、plink
root@DESKTOP-1N42TVH:/home/test# ls cov.txt gwas_test.map gwas_test.ped root@DESKTOP-1N42TVH:/home/test# head cov.txt ## 协变量文件前两列FID、IID； 第三列性别、第四列到最后PC1-PC5 fam1 id1 2 -0.0102664 0.0442708 -0.0658835 0.0251031 0.0126605 fam2 id2 1 0.0421124 -0.0313769 -0.0705913 -0.00235322 0.0344052 fam3 id3 2 -0.0467758 -0.00993805 -0.000487215 0.000353833 0.00282548 fam4 id4 1 -0.00308783 0.0120855 -0.00974726 -0.020038 -0.0383983 fam5 id5 2 -0.0343457 0.00118044 -0.0188934 -0.0217425 -0.0184055 fam6 id6 1 0.00950329 0.0292526 -0.00076269 -0.00176404 -0.0310272 fam7 id7 1 -0.0378972 0.0198437 0.048737 0.112635 0.0563696 fam8 id8 1 -0.031701 0.00046604 -0.00252424 0.0036959 -0.00241191 fam9 id9 1 0.0178986 0.00661469 0.0663559 -0.0156097 -0.012672 fam10 id10 1 -0.0461441 0.0144468 0.0127385 -0.00764761 -0.0210643 root@DESKTOP-1N42TVH:/home/test# plink --file gwas_test --covar cov.txt --covar-number 1-6 --linear --out result root@DESKTOP-1N42TVH:/home/test# ls ## --covar-number 1-6 指的是性别和前五个主成分（自动跳过FID和IID） cov.txt gwas_test.map gwas_test.ped result.assoc.linear result.log root@DESKTOP-1N42TVH:/home/test# head result.assoc.linear CHR SNP BP A1 TEST NMISS BETA STAT P 1 snp1 2802 G ADD 541 -1.083 -0.1411 0.8878 1 snp1 2802 G COV1 541 -34.49 -5.496 6.021e-08 1 snp1 2802 G COV2 541 653.1 8.933 6.714e-18 1 snp1 2802 G COV3 541 213.2 2.929 0.003547 1 snp1 2802 G COV4 541 114.5 1.576 0.1156 1 snp1 2802 G COV5 541 13.96 0.1918 0.848 1 snp1 2802 G COV6 541 69.38 0.9562 0.3394 1 snp2 2823 T ADD 541 9.535 1.038 0.2997 1 snp2 2823 T COV1 541 -34.75 -5.543 4.674e-08
002、gemma
root@DESKTOP-1N42TVH:/home/test# ls cov.txt gwas_test.bed gwas_test.bim gwas_test.fam root@DESKTOP-1N42TVH:/home/test# head cov.txt ## 协变量文件， 第一列为1； 第二列为性别； 第三至最后一列为PCA 1 2 -0.0102664 0.0442708 -0.0658835 0.0251031 0.0126605 1 1 0.0421124 -0.0313769 -0.0705913 -0.00235322 0.0344052 1 2 -0.0467758 -0.00993805 -0.000487215 0.000353833 0.00282548 1 1 -0.00308783 0.0120855 -0.00974726 -0.020038 -0.0383983 1 2 -0.0343457 0.00118044 -0.0188934 -0.0217425 -0.0184055 1 1 0.00950329 0.0292526 -0.00076269 -0.00176404 -0.0310272 1 1 -0.0378972 0.0198437 0.048737 0.112635 0.0563696 1 1 -0.031701 0.00046604 -0.00252424 0.0036959 -0.00241191 1 1 0.0178986 0.00661469 0.0663559 -0.0156097 -0.012672 1 1 -0.0461441 0.0144468 0.0127385 -0.00764761 -0.0210643 root@DESKTOP-1N42TVH:/home/test# /home/software/gemma-0.98.5-linux-static-AMD64 -bfile gwas_test -gk -o kin root@DESKTOP-1N42TVH:/home/test# /home/software/gemma-0.98.5-linux-static-AMD64 -bfile gwas_test -k output/kin.cXX.txt -c cov.txt -lm -o result
root@DESKTOP-1N42TVH:/home/test# head output/result.assoc.txt ## 结果文件 chr rs ps n_mis n_obs allele1 allele0 af beta se p_wald 1 snp1 2802 0 541 G T 0.099 -1.082833e+00 7.674582e+00 8.878495e-01 1 snp2 2823 0 541 T C 0.063 9.534796e+00 9.185000e+00 2.997019e-01 1 snp3 4512 0 541 G A 0.067 1.283873e+01 8.966175e+00 1.527564e-01 1 snp4 16529 0 541 T C 0.055 8.905339e+00 1.019784e+01 3.829161e-01 1 snp5 16578 0 541 G C 0.065 -6.530092e+00 9.144376e+00 4.754717e-01 1 snp6 16579 0 541 C A 0.275 -3.613338e+00 5.192970e+00 4.868490e-01 1 snp7 16635 0 541 G C 0.088 8.206132e+00 7.909573e+00 2.999762e-01 1 snp8 20879 0 541 T G 0.130 8.057337e+00 6.678232e+00 2.281571e-01 1 snp9 20908 0 541 C T 0.167 1.355591e+00 6.265772e+00 8.287988e-01
标签：gwas,01,plink,gemma,00,541,test,home 来源： https://www.cnblogs.com/liujiaxin2018/p/16464408.html