{"id":79143,"date":"2026-03-01T08:48:50","date_gmt":"2026-03-01T00:48:50","guid":{"rendered":"https:\/\/www.wsisp.com\/helps\/79143.html"},"modified":"2026-03-01T08:48:50","modified_gmt":"2026-03-01T00:48:50","slug":"gwas%e5%88%86%e6%9e%90%e9%81%bf%e5%9d%91%e6%8c%87%e5%8d%97%ef%bc%9a%e6%88%91%e5%9c%a8ubuntu%e6%9c%8d%e5%8a%a1%e5%99%a8%e4%b8%8a%e8%b8%a9%e8%bf%87%e7%9a%847%e4%b8%aa%e7%8e%af%e5%a2%83%e9%85%8d%e7%bd%ae","status":"publish","type":"post","link":"https:\/\/www.wsisp.com\/helps\/79143.html","title":{"rendered":"GWAS\u5206\u6790\u907f\u5751\u6307\u5357\uff1a\u6211\u5728Ubuntu\u670d\u52a1\u5668\u4e0a\u8e29\u8fc7\u76847\u4e2a\u73af\u5883\u914d\u7f6e\u5751"},"content":{"rendered":"

GWAS\u5206\u6790\u73af\u5883\u642d\u5efa\u5b9e\u6218：Ubuntu\u670d\u52a1\u5668\u907f\u5751\u624b\u518c<\/h2>\n

\u5f53\u6211\u5728\u5b9e\u9a8c\u5ba4\u7b2c\u4e00\u6b21\u5c1d\u8bd5\u642d\u5efaGWAS\u5206\u6790\u73af\u5883\u65f6，\u672c\u4ee5\u4e3a\u6309\u7167\u6559\u7a0b\u4e00\u6b65\u6b65\u64cd\u4f5c\u5c31\u80fd\u987a\u5229\u5b8c\u6210\u3002\u7136\u800c\u73b0\u5b9e\u7ed9\u4e86\u6211\u4e00\u8bb0\u54cd\u4eae\u7684\u8033\u5149\u2014\u2014\u4ece\u8f6f\u4ef6\u5b89\u88c5\u5230\u6743\u9650\u914d\u7f6e，\u4ece\u4f9d\u8d56\u7f3a\u5931\u5230\u8def\u5f84\u9519\u8bef，\u51e0\u4e4e\u6bcf\u4e00\u6b65\u90fd\u8e29\u4e86\u5751\u3002\u8fd9\u7bc7\u6587\u7ae0\u8bb0\u5f55\u4e86\u6211\u4ece\u96f6\u5f00\u59cb\u642d\u5efaGWAS\u5206\u6790\u73af\u5883（Plink\/vcftools\/R\u5de5\u5177\u94fe）\u8fc7\u7a0b\u4e2d\u9047\u5230\u7684\u4e03\u4e2a\u5178\u578b\u95ee\u9898\u53ca\u5176\u89e3\u51b3\u65b9\u6848，\u5e0c\u671b\u80fd\u5e2e\u52a9\u540e\u6765\u7684\u751f\u4fe1\u5de5\u7a0b\u5e08\u5c11\u8d70\u5f2f\u8def\u3002<\/p>\n

1. Conda\u5b89\u88c5\u5931\u8d25：\u6e90\u914d\u7f6e\u4e0e\u955c\u50cf\u9009\u62e9<\/h3>\n

\u5f88\u591aGWAS\u5de5\u5177\u63a8\u8350\u4f7f\u7528conda\u5b89\u88c5，\u4f46\u76f4\u63a5\u8fd0\u884cconda install -c bioconda plink\u5f80\u5f80\u4f1a\u9047\u5230\u4e0b\u8f7d\u901f\u5ea6\u6162\u751a\u81f3\u5931\u8d25\u7684\u95ee\u9898\u3002\u8fd9\u662f\u56e0\u4e3a\u9ed8\u8ba4\u7684conda\u6e90\u53ef\u80fd\u5bf9\u56fd\u5185\u7528\u6237\u4e0d\u53cb\u597d\u3002<\/p>\n

\u89e3\u51b3\u65b9\u6848\u5206\u4e09\u6b65\u8d70：<\/p>\n

  • \u9996\u5148\u914d\u7f6e\u6e05\u534e\u955c\u50cf\u6e90：<\/li>\n

    conda config –add channels https:\/\/mirrors.tuna.tsinghua.edu.cn\/anaconda\/pkgs\/free\/
    \nconda config –add channels https:\/\/mirrors.tuna.tsinghua.edu.cn\/anaconda\/pkgs\/main\/
    \nconda config –add channels https:\/\/mirrors.tuna.tsinghua.edu.cn\/anaconda\/cloud\/bioconda\/
    \nconda config –set show_channel_urls yes<\/p>\n

  • \u5982\u679c\u4ecd\u7136\u5931\u8d25，\u53ef\u4ee5\u5c1d\u8bd5\u6307\u5b9a\u7248\u672c\u5b89\u88c5：<\/li>\n

    conda install plink=1.90b6.21<\/p>\n

  • \u6700\u540e\u6e05\u9664\u7f13\u5b58\u5e76\u91cd\u8bd5：<\/li>\n

    conda clean –all<\/p>\n

    \u63d0\u793a：\u67d0\u4e9b\u60c5\u51b5\u4e0b\u53ef\u80fd\u9700\u8981\u5148\u521b\u5efa\u72ec\u7acb\u73af\u5883\u518d\u5b89\u88c5，\u907f\u514d\u4e0e\u5df2\u6709\u5305\u51b2\u7a81\u3002<\/p>\n

    2. \u7cfb\u7edf\u4f9d\u8d56\u7f3a\u5931：apt\u6e90\u4f18\u5316\u4e0e\u57fa\u7840\u5e93\u5b89\u88c5<\/h3>\n

    \u5373\u4f7fconda\u5b89\u88c5\u6210\u529f，\u8fd0\u884c\u65f6\u4ecd\u53ef\u80fd\u62a5\u9519\u7f3a\u5c11\u7cfb\u7edf\u5e93\u3002\u8fd9\u662f\u56e0\u4e3a\u8bb8\u591a\u751f\u7269\u4fe1\u606f\u5b66\u5de5\u5177\u4f9d\u8d56\u5e95\u5c42C\/C++\u5e93\u3002<\/p>\n

    \u5e38\u89c1\u7f3a\u5931\u4f9d\u8d56\u53ca\u5b89\u88c5\u547d\u4ee4：<\/p>\n\n\u4f9d\u8d56\u5305\u4f5c\u7528\u5b89\u88c5\u547d\u4ee4<\/tr>\n\n\n\n\n\n
    zlib1g-dev<\/td>\n\u538b\u7f29\u5e93\u652f\u6301<\/td>\nsudo apt install zlib1g-dev<\/td>\n<\/tr>\n
    libbz2-dev<\/td>\nBZip2\u538b\u7f29\u652f\u6301<\/td>\nsudo apt install libbz2-dev<\/td>\n<\/tr>\n
    liblzma-dev<\/td>\nLZMA\u538b\u7f29\u652f\u6301<\/td>\nsudo apt install liblzma-dev<\/td>\n<\/tr>\n
    libcurl4-openssl-dev<\/td>\n\u7f51\u7edc\u8bf7\u6c42\u652f\u6301<\/td>\nsudo apt install libcurl4-openssl-dev<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

    \u4e3a\u63d0\u9ad8\u5b89\u88c5\u6210\u529f\u7387，\u5efa\u8bae\u5148\u66f4\u65b0apt\u6e90：<\/p>\n

    sudo sed -i 's\/archive.ubuntu.com\/mirrors.aliyun.com\/g' \/etc\/apt\/sources.list
    \nsudo apt update<\/p>\n

    3. \u624b\u52a8\u5b89\u88c5PLINK：\u8def\u5f84\u914d\u7f6e\u9677\u9631<\/h3>\n

    \u5f53conda\u5b89\u88c5\u4e0d\u53ef\u884c\u65f6，\u624b\u52a8\u5b89\u88c5PLINK\u662f\u5907\u9009\u65b9\u6848\u3002\u4f46\u8fd9\u91cc\u6709\u51e0\u4e2a\u5173\u952e\u70b9\u5bb9\u6613\u51fa\u9519：<\/p>\n

  • \u4e0b\u8f7d\u5730\u5740\u53ef\u80fd\u53d8\u66f4，\u6700\u65b0\u7248\u5e94\u53bb\u5b98\u7f51\u786e\u8ba4<\/li>\n
  • \u89e3\u538b\u8def\u5f84\u4e0d\u80fd\u5305\u542b\u7a7a\u683c\u6216\u7279\u6b8a\u5b57\u7b26<\/li>\n
  • \u73af\u5883\u53d8\u91cf\u914d\u7f6e\u9700\u8981\u751f\u6548<\/li>\n

    \u6b63\u786e\u64cd\u4f5c\u6d41\u7a0b：<\/p>\n

    # \u4e0b\u8f7d\u6700\u65b0\u7248PLINK
    \nwget https:\/\/s3.amazonaws.com\/plink1-assets\/plink_linux_x86_64_latest.zip<\/p>\n

    # \u89e3\u538b\u5230\u6307\u5b9a\u76ee\u5f55
    \nunzip plink_linux_x86_64_latest.zip -d ~\/software\/plink<\/p>\n

    # \u6c38\u4e45\u6dfb\u52a0\u73af\u5883\u53d8\u91cf
    \necho 'export PATH=$PATH:~\/software\/plink' >> ~\/.bashrc
    \nsource ~\/.bashrc<\/p>\n

    \u9a8c\u8bc1\u5b89\u88c5\u662f\u5426\u6210\u529f：<\/p>\n

    plink –version<\/p>\n

    \u6ce8\u610f：\u5982\u679c\u4f7f\u7528\u975ebash\u7ec8\u7aef（\u5982zsh），\u9700\u8981\u4fee\u6539\u5bf9\u5e94\u7684\u914d\u7f6e\u6587\u4ef6（\u5982.zshrc）<\/p>\n

    4. VCFtools\u5b89\u88c5：\u6743\u9650\u4e0e\u7248\u672c\u517c\u5bb9\u6027\u95ee\u9898<\/h3>\n

    \u867d\u7136\u53ef\u4ee5\u901a\u8fc7sudo apt install vcftools\u5b89\u88c5，\u4f46\u7cfb\u7edf\u4ed3\u5e93\u4e2d\u7684\u7248\u672c\u53ef\u80fd\u8f83\u65e7\u3002\u63a8\u8350\u4ee5\u4e0b\u4e24\u79cd\u5b89\u88c5\u65b9\u5f0f：<\/p>\n

    \u65b9\u6848\u4e00：\u6e90\u7801\u7f16\u8bd1\u5b89\u88c5（\u83b7\u53d6\u6700\u65b0\u529f\u80fd）<\/p>\n

    wget https:\/\/github.com\/vcftools\/vcftools\/releases\/download\/v0.1.16\/vcftools-0.1.16.tar.gz
    \ntar -zxvf vcftools-0.1.16.tar.gz
    \ncd vcftools-0.1.16
    \n.\/autogen.sh
    \n.\/configure
    \nmake
    \nsudo make install<\/p>\n

    \u65b9\u6848\u4e8c：\u4f7f\u7528\u9884\u7f16\u8bd1\u4e8c\u8fdb\u5236（\u5feb\u901f\u90e8\u7f72）<\/p>\n

    wget https:\/\/github.com\/vcftools\/vcftools\/releases\/download\/v0.1.16\/vcftools_0.1.16-1_amd64.deb
    \nsudo dpkg -i vcftools_0.1.16-1_amd64.deb<\/p>\n

    \u5e38\u89c1\u95ee\u9898\u6392\u67e5：<\/p>\n

      \n
    • \u5982\u679c\u62a5\u9519"perl: warning: Setting locale failed"，\u8fd0\u884c：export LC_ALL=C\n<\/li>\n
    • \u5982\u679c\u62a5\u9519"make: command not found"，\u9700\u8981\u5148\u5b89\u88c5build-essential：sudo apt install build-essential\n<\/li>\n<\/ul>\n

      5. R\u73af\u5883\u914d\u7f6e：\u5305\u7ba1\u7406\u4e0e\u955c\u50cf\u4f18\u5316<\/h3>\n

      GWAS\u5206\u6790\u6700\u540e\u9636\u6bb5\u901a\u5e38\u9700\u8981R\u8fdb\u884c\u7edf\u8ba1\u5206\u6790\u548c\u53ef\u89c6\u5316，\u4f46R\u5305\u5b89\u88c5\u7ecf\u5e38\u9047\u5230\u4f9d\u8d56\u95ee\u9898\u3002<\/p>\n

      \u4f18\u5316R\u73af\u5883\u914d\u7f6e\u7684\u6b65\u9aa4：<\/p>\n

    • \u9996\u5148\u5b89\u88c5\u6700\u65b0\u7248R：<\/li>\n

      sudo apt-key adv –keyserver keyserver.ubuntu.com –recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
      \nsudo add-apt-repository 'deb https:\/\/cloud.r-project.org\/bin\/linux\/ubuntu focal-cran40\/'
      \nsudo apt update
      \nsudo apt install r-base r-base-dev<\/p>\n

    • \u914d\u7f6eCRAN\u955c\u50cf：<\/li>\n

      # \u5728R\u4e2d\u6267\u884c
      \noptions(repos = c(CRAN = "https:\/\/mirrors.tuna.tsinghua.edu.cn\/CRAN\/"))<\/p>\n

    • \u5b89\u88c5\u5fc5\u8981GWAS\u5206\u6790\u5305：<\/li>\n

      install.packages(c("qqman", "ggplot2", "data.table"))<\/p>\n

      \u5bf9\u4e8eBioconductor\u5305，\u4f7f\u7528：<\/p>\n

      if (!require("BiocManager", quietly = TRUE))
      \n install.packages("BiocManager")
      \nBiocManager::install("SNPRelate")<\/p>\n

      6. \u6587\u4ef6\u6743\u9650\u7ba1\u7406：\u591a\u7528\u6237\u73af\u5883\u4e0b\u7684\u5b89\u5168\u7b56\u7565<\/h3>\n

      \u5728\u56e2\u961f\u534f\u4f5c\u73af\u5883\u4e2d，\u4e0d\u5f53\u7684\u6587\u4ef6\u6743\u9650\u4f1a\u5bfc\u81f4\u5206\u6790\u6d41\u7a0b\u4e2d\u65ad\u3002\u4ee5\u4e0b\u662f\u63a8\u8350\u7684\u6743\u9650\u7ba1\u7406\u65b9\u6848：<\/p>\n

      \u76ee\u5f55\u7ed3\u6784\u5efa\u8bae：<\/p>\n

      \/project\/
      \n \u251c\u2500\u2500 gwas_data\/ # 775，\u7ec4\u53ef\u8bfb\u5199
      \n \u251c\u2500\u2500 software\/ # 755，\u53ea\u8bfb
      \n \u2514\u2500\u2500 results\/ # 777，\u4e34\u65f6\u5171\u4eab<\/p>\n

      \u5173\u952e\u547d\u4ee4：<\/p>\n

      # \u521b\u5efa\u5171\u4eab\u7ec4
      \nsudo groupadd gwas_team<\/p>\n

      # \u6dfb\u52a0\u7528\u6237\u5230\u7ec4
      \nsudo usermod -a -G gwas_team user1
      \nsudo usermod -a -G gwas_team user2<\/p>\n

      # \u8bbe\u7f6e\u76ee\u5f55\u6743\u9650
      \nsudo chgrp -R gwas_team \/project
      \nsudo chmod -R 775 \/project\/gwas_data<\/p>\n

      \u5bf9\u4e8econda\u73af\u5883，\u53ef\u4ee5\u4f7f\u7528：<\/p>\n

      conda create –prefix \/shared\/conda_envs\/gwas python=3.8
      \nconda config –set env_prompt '({name}) '<\/p>\n

      7. \u5b58\u50a8\u4f18\u5316：\u5927\u6587\u4ef6\u5904\u7406\u6280\u5de7<\/h3>\n

      GWAS\u5206\u6790\u6d89\u53ca\u5927\u91cfVCF\u548c\u4e2d\u95f4\u6587\u4ef6，\u4e0d\u5f53\u5904\u7406\u4f1a\u5bfc\u81f4\u78c1\u76d8\u7a7a\u95f4\u8fc5\u901f\u8017\u5c3d\u3002<\/p>\n

      \u5b9e\u7528\u6280\u5de7：<\/p>\n

        \n
      • \n

        \u4f7f\u7528pigz\u66ff\u4ee3gzip\u52a0\u901f\u538b\u7f29\/\u89e3\u538b：<\/p>\n

        sudo apt install pigz
        \npigz -d pruned_coatColor_maf_geno.vcf.gz # \u89e3\u538b
        \npigz -9 -k pruned_coatColor_maf_geno.vcf # \u6700\u9ad8\u538b\u7f29\u6bd4<\/p>\n<\/li>\n

      • \n

        \u5904\u7406\u5927VCF\u6587\u4ef6\u65f6\u4f7f\u7528\u6d41\u5f0f\u5904\u7406：<\/p>\n

        zcat huge_file.vcf.gz | vcftools –vcf – –plink –out output_prefix<\/p>\n<\/li>\n

      • \n

        \u6e05\u7406\u4e34\u65f6\u6587\u4ef6\u811a\u672c\u793a\u4f8b：<\/p>\n

        #!\/bin\/bash
        \nfind \/tmp -name "plink*" -mtime +1 -exec rm -f {} \\\\;
        \nfind . -name "*.log" -size +10M -exec gzip {} \\\\;<\/p>\n<\/li>\n<\/ul>\n

        \u5b58\u50a8\u65b9\u6848\u5bf9\u6bd4：<\/p>\n\n\u65b9\u6848\u4f18\u70b9\u7f3a\u70b9\u9002\u7528\u573a\u666f<\/tr>\n\n\n\n\n
        \u672c\u5730SSD<\/td>\n\u9ad8\u901fIO<\/td>\n\u5bb9\u91cf\u6709\u9650<\/td>\n\u4e34\u65f6\u6587\u4ef6\u5904\u7406<\/td>\n<\/tr>\n
        \u7f51\u7edc\u5b58\u50a8<\/td>\n\u5171\u4eab\u65b9\u4fbf<\/td>\n\u901f\u5ea6\u8f83\u6162<\/td>\n\u56e2\u961f\u534f\u4f5c<\/td>\n<\/tr>\n
        \u5bf9\u8c61\u5b58\u50a8<\/td>\n\u6269\u5c55\u6027\u5f3a<\/td>\n\u6210\u672c\u8f83\u9ad8<\/td>\n\u957f\u671f\u5f52\u6863<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

        \u5b9e\u6218\u6848\u4f8b：\u5168\u6d41\u7a0b\u73af\u5883\u9a8c\u8bc1<\/h3>\n

        \u4e3a\u786e\u4fdd\u73af\u5883\u914d\u7f6e\u6b63\u786e，\u5efa\u8bae\u8fd0\u884c\u4ee5\u4e0b\u6d4b\u8bd5\u6d41\u7a0b：<\/p>\n

      • \u6570\u636e\u51c6\u5907：<\/li>\n

        wget https:\/\/de.cyverse.org\/dl\/d\/E0A502CC-F806-4857-9C3A-BAEAA0CCC694\/pruned_coatColor_maf_geno.vcf.gz
        \ngunzip pruned_coatColor_maf_geno.vcf.gz<\/p>\n

      • \u683c\u5f0f\u8f6c\u6362\u6d4b\u8bd5：<\/li>\n

        vcftools –vcf pruned_coatColor_maf_geno.vcf –plink –out test_output<\/p>\n

      • PLINK\u4e8c\u8fdb\u5236\u8f6c\u6362：<\/li>\n

        plink –file test_output –make-bed –out test_binary<\/p>\n

      • R\u7ed8\u56fe\u6d4b\u8bd5：<\/li>\n

        library(qqman)
        \ntest_data <- data.frame(CHR=1, BP=1:100, P=runif(100))
        \nmanhattan(test_data)<\/p>\n

        \u5982\u679c\u4ee5\u4e0a\u6b65\u9aa4\u90fd\u80fd\u987a\u5229\u5b8c\u6210，\u8bf4\u660e\u57fa\u7840\u73af\u5883\u5df2\u7ecf\u914d\u7f6e\u6b63\u786e\u3002\u5728\u5b9e\u9645\u9879\u76ee\u4e2d，\u6211\u4eec\u56e2\u961f\u53d1\u73b0\u6700\u8017\u65f6\u7684\u5f80\u5f80\u4e0d\u662f\u5206\u6790\u672c\u8eab，\u800c\u662f\u89e3\u51b3\u5404\u79cd\u73af\u5883\u95ee\u9898\u3002\u6709\u4e00\u6b21\u4e3a\u4e86\u8c03\u8bd5\u4e00\u4e2aperl\u811a\u672c\u7684\u7f16\u7801\u95ee\u9898，\u6211\u4eec\u82b1\u4e86\u6574\u6574\u4e24\u5929\u65f6\u95f4，\u6700\u540e\u53d1\u73b0\u53ea\u662fLC_ALL\u73af\u5883\u53d8\u91cf\u8bbe\u7f6e\u4e0d\u5f53\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"

        GWAS\u5206\u6790\u73af\u5883\u642d\u5efa\u5b9e\u6218：Ubuntu\u670d\u52a1\u5668\u907f\u5751\u624b\u518c
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