{"id":25563,"date":"2024-01-22T17:04:49","date_gmt":"2024-01-22T09:04:49","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=25563"},"modified":"2024-01-22T17:04:50","modified_gmt":"2024-01-22T09:04:50","slug":"%e4%b8%a4%e5%88%86%e9%92%9f%e5%ad%a6%e4%bc%9a%e5%88%86%e6%9e%90%e5%8f%98%e5%bc%82%e6%a3%80%e6%b5%8b%e7%bb%93%e6%9e%9c","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=25563","title":{"rendered":"\u4e24\u5206\u949f\u5b66\u4f1a\u5206\u6790\u53d8\u5f02\u68c0\u6d4b\u7ed3\u679c"},"content":{"rendered":"

\u4e0a\u4e00\u6b21\u5c0f\u679c\u7ed9\u5927\u5bb6\u8be6\u7ec6\u5730\u5206\u4eab\u4e86\u53d8\u5f02\u68c0\u6d4b\u7684\u6d41\u7a0b\uff0c\u8fd9\u6b21\u4e3a\u4e86\u8ba9\u5c0f\u4f19\u4f34\u4eec\u7406\u89e3\u7684\u66f4\u900f\u5f7b\uff0c\u5c0f\u679c\u5728\u8fd9\u91cc\u4e3a\u5927\u5bb6\u89e3\u8bfb\u4e00\u4e0b\u53d8\u5f02\u68c0\u6d4b\u7ed3\u679c\uff0c\u5e9f\u8bdd\u4e0d\u591a\u8bf4\uff0c\u6211\u4eec\u76f4\u63a5\u5f00\u59cb\u5427\uff1a<\/p>\n

VCF\u6587\u4ef6<\/h3>\n

FreeBayes\u751f\u6210\u7684VCF\uff08Variant Call Format\uff09\u6587\u4ef6\u662f\u4e00\u79cd\u5e38\u7528\u7684\u63cf\u8ff0\u57fa\u56e0\u7ec4\u53d8\u5f02\u4fe1\u606f\u7684\u6807\u51c6\u6587\u4ef6\u683c\u5f0f\uff0c\u7528\u4e8e\u63cf\u8ff0SNP\u3001INDEL\u548cSV\u7ed3\u679c\uff0c\u8fd9\u91cc\u5c0f\u679c\u4ee5\u4e0a\u6b21\u6211\u4eec\u7528FreeBayes\u5904\u7406\u5f97\u5230\u7684\u7ed3\u679c\u6587\u4ef6\u505a\u5982\u4e0b\u8bf4\u660e\uff1a<\/p>\n

<\/p>\n

\u5728VCF\u6587\u4ef6\u4e2d\uff0c\u6bcf\u4e00\u884c\u8868\u793a\u4e00\u4e2a\u4f4d\u70b9\u7684\u4fe1\u606f\uff0c\u5217\u540d\u548c\u89e3\u91ca\u5982\u4e0b\uff1a<\/p>\n

    \n
  1. CHROM\uff1a\u67d3\u8272\u4f53\u540d\u79f0\uff0c\u8868\u793a\u8be5\u4f4d\u70b9\u6240\u5728\u7684\u67d3\u8272\u4f53\u3002<\/li>\n
  2. POS\uff1a\u4f4d\u70b9\u5728\u67d3\u8272\u4f53\u4e0a\u7684\u4f4d\u7f6e\uff0c\u4ee5\u57fa\u56e0\u7ec4\u5750\u6807\u5f62\u5f0f\u7ed9\u51fa\u3002<\/li>\n
  3. ID\uff1a\u4f4d\u70b9\u7684\u552f\u4e00\u6807\u8bc6\u7b26\uff0c\u53ef\u4ee5\u662frs\u53f7\uff08\u5728dbSNP\u6570\u636e\u5e93\u4e2d\u6ce8\u518c\u7684SNP\u7684\u6807\u8bc6\u7b26\uff09\u6216\u5176\u4ed6\u552f\u4e00ID\u3002<\/li>\n
  4. REF\uff1a\u53c2\u8003\u7b49\u4f4d\u57fa\u56e0\uff0c\u8868\u793a\u5728\u8be5\u4f4d\u70b9\u4e0a\u7684\u53c2\u8003\u5e8f\u5217\u3002<\/li>\n
  5. ALT\uff1a\u5907\u9009\u7b49\u4f4d\u57fa\u56e0\uff0c\u8868\u793a\u5728\u8be5\u4f4d\u70b9\u4e0a\u53ef\u80fd\u5b58\u5728\u7684\u5176\u4ed6\u53d8\u5f02\u5e8f\u5217\u3002<\/li>\n
  6. QUAL\uff1a\u8d28\u91cf\u5f97\u5206\uff0c\u8868\u793a\u5bf9\u8be5\u4f4d\u70b9\u7684\u7f6e\u4fe1\u5ea6\u6216\u53ef\u9760\u7a0b\u5ea6\u7684\u4f30\u8ba1\u3002<\/li>\n
  7. FILTER\uff1a\u8fc7\u6ee4\u72b6\u6001\uff0c\u8868\u793a\u8be5\u4f4d\u70b9\u662f\u5426\u901a\u8fc7\u7279\u5b9a\u7684\u8d28\u91cf\u63a7\u5236\u7b5b\u9009\u3002<\/li>\n
  8. INFO\uff1a\u9644\u52a0\u4fe1\u606f\uff0c\u63d0\u4f9b\u5173\u4e8e\u8be5\u4f4d\u70b9\u7684\u989d\u5916\u6ce8\u91ca\u548c\u76f8\u5173\u4fe1\u606f\uff0c\u4ee5\u952e\u503c\u5bf9\u7684\u5f62\u5f0f\u5448\u73b0\u3002<\/li>\n
  9. FORMAT\uff1a\u6837\u672c\u6570\u636e\u683c\u5f0f\uff0c\u6307\u5b9a\u5728VCF\u6587\u4ef6\u7684\u540e\u7eed\u5217\u4e2d\u5982\u4f55\u89e3\u91ca\u6bcf\u4e2a\u6837\u672c\u7684\u57fa\u56e0\u578b\u4fe1\u606f\u3002<\/li>\n
  10. unknown\uff1a\u6837\u672c\u6570\u636e\u5217\uff0c\u6bcf\u4e2a\u6837\u672c\u5360\u636e\u4e00\u5217\uff0c\u8868\u793a\u5bf9\u5e94\u4f4d\u70b9\u7684\u8be5\u6837\u672c\u7684\u57fa\u56e0\u578b\u548c\u5176\u4ed6\u76f8\u5173\u4fe1\u606f\u3002<\/li>\n<\/ol>\n

    \u5c0f\u679c\u63d0\u793a\uff1a\u56e0\u4e3a\u5907\u5fd8\u5f55\u663e\u793a\u5c40\u9650\u95ee\u9898\uff0cINFO\u5217\u5185\u5bb9\u592a\u591a\uff0c\u6240\u4ee5\u4e0b\u56fe\u84dd\u8272\u5185\u5bb9\u662fINFO\u5217\u7684\u4fe1\u606f\uff0c\u663e\u793a\u5927\u5c0f\u653e\u7f29\u540e\u7684\u6392\u5217\u65b9\u5f0f\u4e3a\u672c\u5e94\u7684\u6392\u5217\u65b9\u5f0f\uff1a<\/p>\n

    <\/p>\n

    <\/p>\n

    \u63d0\u53d6SNP\u4ee5\u53caINDEL<\/h4>\n

    \u5728VCF\u6587\u4ef6\u4e2d\uff0cINFO\u5217\u662f\u7528\u6765\u6ce8\u91ca\u6bcf\u4e2a\u53d8\u5f02\u8bb0\u5f55\u7684\u4fe1\u606f\u3002\u5176\u4e2d\uff0ctag\u662fINFO\u5217\u4e2d\u7684\u4e00\u4e2a\u5b57\u6bb5\uff0c\u4e13\u95e8\u7528\u6765\u8868\u793a\u4e0d\u540c\u7c7b\u578b\u7684\u7a81\u53d8\u3002\u4e0b\u9762\u662f\u4e0d\u540c\u6807\u7b7e\u7684\u542b\u4e49\uff1a<\/p>\n

      \n
    • SNP\uff08Single Nucleotide Polymorphism\uff09\uff1a\u8868\u793a\u5355\u6838\u82f7\u9178\u591a\u6001\u6027\uff0c\u5373\u5728\u57fa\u56e0\u7ec4\u4e2d\u5b58\u5728\u5355\u4e2a\u78b1\u57fa\u53d1\u751f\u66ff\u6362\u7684\u53d8\u5f02\u3002<\/li>\n
    • INS\uff08Insertion\uff09\uff1a\u8868\u793a\u63d2\u5165\u4e8b\u4ef6\uff0c\u5373\u76f8\u5bf9\u4e8e\u53c2\u8003\u57fa\u56e0\u7ec4\uff0c\u5728\u6837\u672c\u57fa\u56e0\u7ec4\u4e2d\u63d2\u5165\u4e86\u4e00\u6bb5\u65b0\u7684\u78b1\u57fa\u5e8f\u5217\u3002<\/li>\n
    • DEL\uff08Deletion\uff09\uff1a\u8868\u793a\u7f3a\u5931\u4e8b\u4ef6\uff0c\u5373\u76f8\u5bf9\u4e8e\u53c2\u8003\u57fa\u56e0\u7ec4\uff0c\u6837\u672c\u57fa\u56e0\u7ec4\u4e2d\u5220\u9664\u4e86\u4e00\u6bb5\u78b1\u57fa\u5e8f\u5217\u3002<\/li>\n
    • MNP\uff08Multiple Nucleotide Polymorphism\uff09\uff1a\u8868\u793a\u8fde\u7eed\u4e24\u4e2aSNP\u4f4d\u70b9\u7684\u53d8\u5f02\uff0c\u4f8b\u5982\uff0c\u53c2\u8003\u57fa\u56e0\u7ec4\u4e2d\u7684AT\u88ab\u66ff\u6362\u4e3a\u6837\u672c\u57fa\u56e0\u7ec4\u4e2d\u7684CG\u3002<\/li>\n
    • Complex\uff08Composite Insertion and Substitution Events\uff09\uff1a\u8868\u793a\u590d\u5408\u63d2\u5165\u548c\u66ff\u6362\u4e8b\u4ef6\uff0c\u5373\u5728\u6837\u672c\u57fa\u56e0\u7ec4\u4e2d\u540c\u65f6\u53d1\u751f\u4e86\u63d2\u5165\u548c\u66ff\u6362\u7684\u53d8\u5f02\u3002<\/li>\n<\/ul>\n

      \u6839\u636e\u4e0a\u8ff0\u63cf\u8ff0\uff0c\u53ef\u4ee5\u901a\u8fc7\u89e3\u6790VCF\u6587\u4ef6\u5e76\u67e5\u627eINFO\u5217\u4e2d\u7279\u5b9a\u6807\u7b7e\u7684\u503c\u6765\u63d0\u53d6\u4e0d\u540c\u7c7b\u578b\u7684\u7a81\u53d8\u8bb0\u5f55\u3002\u8fd9\u6837\u7684\u5206\u6790\u6709\u52a9\u4e8e\u8fdb\u4e00\u6b65\u7814\u7a76\u548c\u7406\u89e3\u57fa\u56e0\u7ec4\u53d8\u5f02\u5728\u9057\u4f20\u5b66\u548c\u75be\u75c5\u7814\u7a76\u4e2d\u7684\u4f5c\u7528\u3002<\/p>\n

      # \u4f7f\u7528grep\u547d\u4ee4\u4ecefreebayes.vcf\u6587\u4ef6\u4e2d\u63d0\u53d6\u6240\u6709\u7684SNP\uff08\u5355\u6838\u82f7\u9178\u591a\u6001\u6027\uff09\u8bb0\u5f55\uff0c\u5e76\u5c06\u7ed3\u679c\u4fdd\u5b58\u5230\u65b0\u6587\u4ef6freebayes_snp.vcf\u4e2d\u3002
      \ngrep \u2018TYPE=snp\u2019 freebayes.vcf \\> freebayes_snp.vcf<\/p>\n

      INFO\u5217\u8fd8\u6709\u4e24\u79cd\u4fe1\u606f\u6bd4\u8f83\u91cd\u8981\uff0c\u5206\u522b\u662f\uff1a<\/p>\n

      GT\uff1a<\/strong> \u8868\u793a\u8fd9\u4e2a\u6837\u672c\u7684\u57fa\u56e0\u578b\uff0c\u5bf9\u4e8e\u4e00\u4e2a\u4e8c\u500d\u4f53\u751f\u7269\uff0cGT\u503c\u8868\u793a\u7684\u662f\u8fd9\u4e2a\u6837\u672c\u5728\u8fd9\u4e2a\u4f4d\u70b9\u6240\u643a\u5e26\u7684\u4e24\u4e2a\u7b49\u4f4d\u57fa\u56e0\u30020\u8868\u793a\u8ddfREF\u4e00\u6837\uff1b1\u8868\u793a\u8868\u793a\u8ddfALT\u4e00\u6837\uff1b2\u8868\u793a\u7b2c\u4e8c\u4e2aALT\u3002\u5f53\u53ea\u6709\u4e00\u4e2aALT \u7b49\u4f4d\u57fa\u56e0\u7684\u65f6\u5019\uff0c0\/0\u8868\u793a\u7eaf\u548c\u4e14\u8ddfREF\u4e00\u81f4\uff1b0\/1\u8868\u793a\u6742\u5408\uff0c\u4e24\u4e2aallele\u4e00\u4e2a\u662fALT\u4e00\u4e2a\u662fREF\uff1b1\/1\u8868\u793a\u7eaf\u548c\u4e14\u90fd\u4e3aALT<\/p>\n

      DP\uff1a<\/strong> \u8986\u76d6\u5230\u8fd9\u4e2a\u4f4d\u70b9\u7684reads\u6570\u91cf\uff0c\u76f8\u5f53\u4e8e\u8fd9\u4e2a\u4f4d\u70b9\u7684\u6df1\u5ea6\uff08\u5e76\u4e0d\u662f\u6240\u6709\u7684reads\u6570\u91cf\uff0c\u800c\u662f\u8fbe\u5230\u4e00\u5b9a\u8d28\u91cf\u503c\u8981\u6c42\u7684reads\u6570\uff09\u3002<\/p>\n

      \u9650\u4e8e\u7bc7\u5e45\uff0c\u5c0f\u679c\u5c31\u4e0d\u5728\u8fd9\u91cc\u5bf9VCF\u6587\u4ef6\u4e2d\u7684INFO\u5217\u7684\u5177\u4f53\u5185\u5bb9\u6240\u4ee3\u8868\u7684\u542b\u4e49\u505a\u5177\u4f53\u89e3\u91ca\u5566\uff0c\u611f\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u4eec\u53ef\u4ee5\u81ea\u884c\u67e5\u9605\u54e6~\u5c0f\u679c\u5728\u8fd9\u91cc\u7ed9\u5927\u5bb6\u4e3e\u4f8b\u5206\u4eab\u4e00\u4e0b\u4ee5\u4e0b\u8fd9\u5217FORMAT\u5217\u7684\u4fe1\u606f\uff1a<\/p>\n

      <\/p>\n