{"id":24124,"date":"2024-01-10T17:29:15","date_gmt":"2024-01-10T09:29:15","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=24124"},"modified":"2024-01-10T17:29:17","modified_gmt":"2024-01-10T09:29:17","slug":"plink%e8%bd%af%e4%bb%b6%e5%88%9d%e4%bd%93%e9%aa%8c1-%e8%b4%a8%e9%87%8f%e6%8e%a7%e5%88%b6","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=24124","title":{"rendered":"PLINK\u8f6f\u4ef6\u521d\u4f53\u9a8c1–\u8d28\u91cf\u63a7\u5236"},"content":{"rendered":"

GWAS\u5206\u6790\u65f6\uff0c\u62ff\u5230\u57fa\u56e0\u578b\u6570\u636e\uff0c\u62ff\u5230\u8868\u578b\u6570\u636e\u65f6\uff0c\u9996\u5148\u5e94\u8be5\u60f3\u5230\u8981\u5bf9<\/a>\u57fa\u56e0\u578b\u548c\u8868\u578b\u6570\u636e\u7684\u8d28\u91cf\u8fdb\u884c\u68c0\u6d4b\u548c\u63a7\u5236\u3002\u7136\u540e\u518d\u8003\u8651\u8fd9\u7ec4\u6570\u636e\u8be5\u600e\u4e48\u5206\u6790\uff0c\u5982\u4f55\u5206\u6790\u3002\u57fa\u56e0\u578b\u548c\u8868\u578b\u7684\u8d28\u63a7\u662f\u975e\u5e38\u91cd\u8981\u7684\uff0c\u5982\u679c\u6570\u636e\u7684\u8d28\u91cf\u4e0d\u4f73\uff0c\u90a3\u4e48\u8ba1\u7b97\u7684\u7ed3\u679c\u7684\u6709\u6548\u6027\u548c\u51c6\u786e\u6027\u5c31\u65e0\u6cd5\u4fdd\u8bc1\u3002\u5373\u4f7f\u540e\u7eed\u5206\u6790\u7684\u975e\u5e38\u8be6\u7ec6\uff0c\u6700\u540e\u7684\u7ed3\u679c\u4e5f\u8fd8\u662f\u4e0d\u7406\u60f3\u7684\uff0c\u76f8\u5f53\u4e8e\u505a\u4e86\u65e0\u7528\u529f\u3002\u6240\u4ee5\u5bf9\u57fa\u56e0\u578b\u548c\u8868\u578b\u8d28\u63a7\u662f\u81f3\u5173\u91cd\u8981\u7684\u3002\u90a3\u4e48\u5982\u4f55\u5bf9\u6570\u636e\u8d28\u63a7\u5462\uff0c\u9700\u8981\u5bf9\u90a3\u4e9b\u6307\u6807\u8fdb\u884c\u6307\u63a7\u5462\uff1f\u8fd9\u90fd\u662f\u9700\u8981\u6ce8\u610f\u7684\u3002\u4eca\u5929\u548c\u5c0f\u679c\u5b66\u4e60\u4e00\u4e0b\u57fa\u56e0\u7ec4\u6570\u636e\u5982\u4f55\u6e05\u6d17\u3002<\/p>\n

\u9996\u5148\u4ecb\u7ecd\u4e00\u4e0b\u9700\u8981\u5bf9\u90a3\u4e9b\u6307\u6807\u8fdb\u884c\u8d28\u63a7\u3002<\/h3>\n

1.\u4e2a\u4f53\u57fa\u56e0\u5206\u578b\u68c0\u51fa\u7387\uff08call rate\uff09<\/h4>\n

\u6837\u672c\u68c0\u51fa\u7387\uff1a<\/strong>\u662f\u6307\u5bf9\u4e8e\u67d0\u79cd\u6837\u672c\u800c\u8a00\uff0c\u901a\u8fc7\u6d4b\u5e8f\u5e76\u6210\u529f\u5224\u5211\u7684snp\u4e0e\u6240\u6709\u68c0\u51fa\u7684snp\u7684\u6bd4\u503c\uff0c\u901a\u5e38\u6807\u51c6\u572890%\u6216\u4ee5\u4e0a\u3002<\/p>\n

    \n
  1. \u5355\u4e2a\u4f4d\u70b9\u57fa\u56e0\u5206\u578b\u68c0\u51fa\u7387\uff08call rate\uff09<\/strong><\/li>\n<\/ol>\n

    snp\u68c0\u51fa\u7387\uff1a<\/strong>\u6307\u5bf9\u67d0\u4e2asnp\u4f4d\u70b9\u88ab\u6210\u529f\u68c0\u6d4b\u5230\u7684\u6837\u672c\u4e0e\u6240\u6709\u6837\u672c\u6bd4\u503c\uff0c\u4e00\u822c\u8981\u6c42\u572890%\u6216\u4ee5\u4e0a\u3002<\/p>\n

    \u6700\u5c0f\u7b49\u4f4d\u57fa\u56e0\u9891\u7387\uff08Minor Allele Frequency\uff0cMAF\uff09<\/h4>\n

    \u6700\u5c0f\u7b49\u4f4d\u57fa\u56e0\u9891\u7387\uff1a<\/strong>\u5bf9\u90a3\u4e9bMAF\u8f83\u5c0f\u7684snp\uff0c\u80fd\u5f97\u5230\u4fe1\u606f\u91cf\u8f83\u5c11\u800c\u4e14\u76ee\u524d\u5bf9\u8fd9\u4e9bsnp\u68c0\u51fa\u6548\u7387\u4e5f\u4e0d\u9ad8\uff0c\u901a\u5e38\u8981\u6c42maf\u503c\u57285%\u53ca\u4ee5\u4e0a\u3002<\/p>\n

    \u54c8\u4ee3\u6e29\u4f2f\u683c\u5e73\u8861 \uff08Hardy-wenberg Epuilibrium\uff0cHWE\uff09<\/h4>\n

    \u54c8\u4ee3\u6e29\u4f2f\u683c\u5e73\u8861\uff1a<\/strong>HWE\u6709\u52a9\u4e8e\u786e\u5b9a\u54ea\u4e9b\u6709\u660e\u663e\u57fa\u56e0\u5206\u578b\u9519\u8bef\u7684snp\uff0c\u56e0\u6b64\u4e00\u822c\u8981\u6c42\u4f4d\u70b9snp\u7b26\u5408HWE.<\/p>\n

    \u5728PLINK\u4e2d\u505a\u8fd9\u51e0\u6b65\u7684\u8d28\u91cf\u63a7\u5236\uff0c\u53ef\u4ee5\u76f4\u63a5\u4f7f\u7528\u547d\u4ee4+\u53c2\u6570\u5b8c\u6210\u7b5b\u9009\uff0c\u4e5f\u53ef\u4ee5\u4f7f\u7528PLINK\u751f\u6210\u68c0\u6d4b\u7ed3\u679c\u6765\u624b\u52a8\u7b5b\u9009\u3002\u5f53\u7136\uff0c\u4e00\u822c\u5bf9\u6570\u636e\u8981\u6c42\u4e25\u683c\u7684\u5b9e\u9a8c\u90fd\u662f\u5148\u751f\u6210\u7ed3\u679c\uff0c\u7ecf\u8fc7\u67e5\u770b\u4ee5\u540e\u786e\u5b9a\u53c2\u6570\u518d\u4f7f\u7528PLINK\u8fdb\u884c\u7b5b\u9009\u3002<\/p>\n

    \u5177\u4f53\u6765\u8bb2\uff0c\u6839\u636e\u5c0f\u679c\u7684\u4e60\u60ef\u4e00\u822c\u5148\u8fdb\u884c\u4e2a\u4f53\u548cSNP\u7684\u7b5b\u9009\uff0c\u6b21\u7b49\u4f4d\u57fa\u56e0\u9891\u7387\u3001\u54c8\u4ee3\u5e73\u8861\u7684\u68c0\u6d4b\uff0c\u518d\u505a\u4e00\u904d\u4e0a\u8ff0\u7684\u7b5b\u9009\u3002<\/p>\n

    \u5bf9\u4e2a\u4f53\u548cSNP\u7684\u68c0\u6d4b\u548c\u7b5b\u9009<\/strong><\/p>\n

    \u2013missing \u751f\u6210\u4e2a\u4f53\u548cSNP\u7f3a\u5931\u7684\u68c0\u6d4b\u7ed3\u679c\u3002<\/p>\n

    \u4e2a\u4f53\u7f3a\u5931\u4f4d\u70b9\u7ed3\u679c\u6587\u4ef6\u4e3aplink.imiss\uff1a<\/p>\n

    \u7b2c\u4e00\u5217\u4e3a\u5bb6\u7cfbID\uff0c\u7b2c\u4e8c\u5217\u4e3a\u4e2a\u4f53ID\uff0c\u7b2c\u4e09\u5217\u662f\u5426\u8868\u578b\u7f3a\u5931\uff0c\u7b2c\u56db\u5217\u7f3a\u5931\u7684SNP\u4e2a\u6570\uff0c\u7b2c\u4e94\u5217\u603bSNP\u4e2a\u6570\uff0c\u7b2c\u516d\u5217\u7f3a\u5931\u7387\u3002<\/p>\n

    <\/p>\n

    \u5355\u4e2aSNP\u7f3a\u5931\u7684\u7ed3\u679c\u6587\u4ef6\u4e3aplink.lmiss\uff1a<\/p>\n

    \u7b2c\u4e00\u5217\u4e3a\u67d3\u8272\u4f53\uff0c\u7b2c\u4e8c\u5217\u4e3aSNP\u540d\u79f0\uff0c\u7b2c\u4e09\u5217\u4e3a\u7f3a\u5931\u4e2a\u6570\uff0c\u7b2c\u56db\u5217\u4e3a\u603b\u4e2a\u6570\uff0c\u7b2c\u4e94\u5217\u4e3a\u7f3a\u5931\u7387<\/p>\n

    <\/p>\n

    \u54c8\u4ee3\u6e29\u4f2f\u683c\u5e73\u8861<\/strong><\/p>\n

    \u2013hardy \u8ba1\u7b97\u6240\u6709\u4f4d\u70b9\u7684\u54c8\u6e29\u68c0\u6d4b\u7ed3\u679c<\/p>\n

    \u7ed3\u679c\u6587\u4ef6\u4e3aplink.hwe\uff1a<\/p>\n

    \u7b2c\u4e00\u5217\u4e3a\u67d3\u8272\u4f53\uff0c\u7b2c\u4e8c\u5217\u4e3aSNP\u7684ID\uff0c\u7b2c\u4e09\u5217\u4e3aTEST\u7c7b\u578b\uff0c\u7b2c\u56db\u5217A1\u4e3a minor \u4f4d\u70b9\uff0c\u7b2c\u4e94\u5217A2\u4e3a major \u4f4d\u70b9\uff0c\u7b2c\u516d\u5217\u4e3a\u57fa\u56e0\u578b\u5206\u5e03\uff0c\u5bf9\u5e94A1A1, A1A2, A2A2\u7684\u4e2a\u6570\uff0c\u7b2c\u516d\u5217\u4e3a\u89c2\u6d4b\u6742\u5408\u5ea6\u9891\u7387\uff0c\u7b2c\u4e03\u5217\u4e3a\u671f\u671b\u6742\u5408\u5ea6\u9891\u7387\uff0c\u7b2c\u516b\u5217\u4e3a\u54c8\u6e29\u5e73\u8861\u7684\u5361\u65b9\u68c0\u9a8cP<\/em>\u503c\u3002<\/p>\n

    <\/p>\n

    \u6b21\u7b49\u4f4d\u57fa\u56e0\u9891\u7387<\/strong><\/p>\n

    \u2013freq \u8ba1\u7b97\u6bcf\u4e2aSNP\u4f4d\u70b9\u7684\u6b21\u57fa\u56e0\u9891\u7387<\/p>\n

    \u7ed3\u679c\u6587\u4ef6\u4e3aplink.frq\uff1a<\/p>\n

    \u7b2c\u4e00\u5217\u4e3a\u67d3\u8272\u4f53\u53f7\uff0c\u7b2c\u4e8c\u5217\u4e3aSNP ID\uff0c\u7b2c\u4e09\u5217\u4e3a minor \u4f4d\u70b9\uff0c\u7b2c\u56db\u5217\u4e3a major \u4f4d\u70b9\uff0c\u7b2c\u4e94\u5217\u4e3a\u6b21\u7b49\u4f4d\u57fa\u56e0\u9891\u7387\uff0c\u7b2c\u516d\u5217\u4e3a\u7b49\u4f4d\u57fa\u56e0\u89c2\u5bdf\u6570\u3002<\/p>\n

    <\/p>\n

    \u77e5\u9053\u4e86\u68c0\u6d4b\u7684\u7ed3\u679c\u4e00\u5207\u5c31\u597d\u529e\u4e86\uff0c\u63a5\u4e0b\u6765\u4ecb\u7ecd\u4e00\u4e0b\u5404\u4e2a\u6307\u6807\u7684\u8d28\u63a7\u65b9\u6cd5\uff08\u5229\u7528PLINK\u8f6f\u4ef6\uff09<\/h3>\n

    call rate >90%<\/strong><\/p>\n

    plink –file <\/a>1-data-holstein –geno 0.01 –recode –out <\/a>2-data-holstein_qc\u00a0 \u00a0###\u8fd9\u4e00\u6b65\u5c31\u662f\u8981\u6c42snp\u68c0\u51fa\u7387\u8981\u572890%\u4ee5\u4e0a<\/p>\n

    plink –file 1-data-holstein –mind 0.01 –recode –out 3-data-holstein_qc\u00a0 \u00a0##\u8fd9\u6b65\u5c31\u662f\u5bf9\u6837\u672c\u68c0\u51fa\u7387\u8fdb\u884c\u8d28\u63a7\uff0c\u63a7\u5236\u572890%\u4ee5\u4e0a<\/p>\n

    MAF>0.05<\/strong><\/p>\n

    plink –file <\/a>1-data-holstein –maf 0.05 –recode –out 4-data-holstein_qc\u00a0 \u00a0##\u8fd9\u6b65\u662f\u5bf9\u6700\u5c0f\u7b49\u4f4d\u57fa\u56e0\u9891\u7387\u8fdb\u884c\u8d28\u63a7\uff0c\u8981\u6c42\u8981\u5927\u4e8e0.05.<\/p>\n

    HWE < 0.00001<\/strong><\/p>\n

    plink –file 1-data-holstein –hwe 0.00001 –recode –out 5-data-holstein_qc ####\u6b64\u6b65\u8981\u6c42\u54c8\u4ee3\u6e29\u4f2f\u683c\u5e73\u8861\u8981\u5c0f\u4e8e0.00001\u3002<\/p>\n

    \u597d\u4e86\uff0c\u770b\u4e86\u4e0a\u8ff0\u7684\u8d28\u63a7\u6d41\u7a0b\uff0c\u57fa\u672c\u4e0a\u5c31\u80fd\u89e3\u51b3\u95ee\u9898\u4e86\uff0c\u4e0d\u8fc7\u4e00\u6b65\u4e00\u6b65\u7684\u6765\u5f88\u7e41\u7410\uff0c\u53ef\u4ee5\u628a\u6240\u6709\u7684\u8fc7\u7a0b\u5408\u5e76\u5230\u4e00\u8d77\u4f8b\u5982\uff1a<\/h4>\n

    plink –file 1-data-holstein –mind 0.1 –geno 0.1 –maf 0.05 –hwe 0.00001 –recode –out 2-data-holstein_qc\u00a0 \u00a0 \u00a0#\u8fd9\u6761\u7a0d\u5fae\u957f\u4e00\u70b9\u7684\u547d\u4ee4\u5c31\u628a\u6240\u6709\u6307\u6807\u7684\u5168\u90e8\u90fd\u5305\u542b\u4e86\u53ef\u4ee5\u4e00\u6b65\u5c31\u51fa\u6765\u8d28\u63a7\u7ed3\u679c\u3002<\/p>\n

    \u5728\u751f\u6210\u7684\u65e5\u5fd7\u6587\u4ef6\u4e2d\u53ef\u4ee5\u67e5\u770b\u8d28\u63a7\u7ed3\u679c\u3002<\/p>\n

    <\/p>\n

    \u4e0a\u8ff0\u5c31\u662f\u57fa\u56e0\u578b\u548c\u8868\u578b\u8d28\u63a7\u7684\u5185\u5bb9\uff0c\u8bf7\u7ed3\u5408\u81ea\u5df1\u7684\u6570\u636e\u60c5\u51b5\u9009\u62e9\u8d28\u63a7\u6307\u6807\u548c\u8d28\u63a7\u6307\u6807\u7684\u9608\u503c\u3002\u5b66\u5b8c\u4e86\u8fd9\u6b3e\u8f6f\u4ef6\u662f\u4e0d\u662f\u60f3\u9a6c\u4e0a\u64cd\u4f5c\u4e00\u756a\uff0c\u5927\u5bb6\u53ef\u4ee5\u6d4b\u8bd5\u4e00\u4e0b\uff0c\u8ba9\u77e5\u8bc6\u66f4\u52a0\u7262\u56fa\u3002<\/p>\n

    \u540e\u9762\u5c0f\u679c\u5c06\u7ed9\u5c0f\u4f19\u4f34\u4eec\u7ee7\u7eed\u5206\u4eabPLINK\u8f6f\u4ef6\u8fdb\u884cGWAS\u5206\u6790\u64cd\u4f5c\u6d41\u7a0b\uff0c\u5982\u6709\u9700\u8981\u7ee7\u7eed\u5173\u6ce8\u751f\u4fe1\u679c\u548c\u4e91\u751f\u4fe1\u751f\u7269\u4fe1\u606f\u5b66\u5e73\u53f0\uff08\u00a0\u00a0http:\/\/www.biocloudservice.com\/home.html<\/a>\uff09<\/p>\n","protected":false},"excerpt":{"rendered":"

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