{"id":71588,"date":"2026-11-15T01:24:15","date_gmt":"2026-11-14T17:24:15","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=71588"},"modified":"2026-11-15T01:24:15","modified_gmt":"2026-11-14T17:24:15","slug":"graphaligner-high-mapq-split-gaf-graph-missing-allele","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/graphaligner-high-mapq-split-gaf-graph-missing-allele\/","title":{"rendered":"GraphAligner \u5b9e\u8dd1\uff5c\u4e24\u6bb5\u6bd4\u5bf9\u7684 MAPQ \u90fd\u662f 60\uff0c\u4e3a\u4ec0\u4e48\u4e00\u6761 3500 bp \u8bfb\u6bb5\u4e2d\u95f4\u4ecd\u6709 600 bp \u6ca1\u6709\u89e3\u91ca\uff1f"},"content":{"rendered":"
\n

\u7528\u957f\u8bfb\u6bb5\u9a8c\u8bc1\u6cdb\u57fa\u56e0\u7ec4\u56fe\u65f6\uff0c\u4e00\u6761\u8bfb\u6bb5\u53ef\u80fd\u7ed9\u51fa\u597d\u51e0\u884c\u56fe\u6bd4\u5bf9\u3002\u82e5\u6bcf\u884c\u6620\u5c04\u8d28\u91cf\u90fd\u5f88\u9ad8\u3001\u7f16\u8f91\u8ddd\u79bb\u90fd\u662f\u96f6\uff0c\u80fd\u5426\u636e\u6b64\u8ba4\u4e3a\u8fd9\u6761\u8bfb\u6bb5\u4ece\u5934\u5230\u5c3e\u90fd\u88ab\u56fe\u89e3\u91ca\u4e86\uff1f\u6211\u4eec\u4ece\u4e00\u5f20\u6709\u4e24\u6761\u5206\u652f\u7684\u56fe\u91cc\u63d0\u53d6\u540c\u4e00\u6279\u6a21\u62df\u8bfb\u6bb5\uff0c\u968f\u540e\u53ea\u4ece\u76ee\u6807\u56fe\u4e2d\u79fb\u53bb\u5176\u4e2d\u4e00\u6761\u5206\u652f\uff0c\u518d\u7528 GraphAligner \u6bd4\u5bf9\u3002\u4e00\u4e2a\u6700\u663e\u773c\u7684\u53d8\u5316\u662f\uff0c\u6bd4\u5bf9\u8868\u53cd\u800c\u591a\u4e86\u4e00\u884c\u3002\u6309\u67e5\u8be2\u8bfb\u6bb5\u7684\u5750\u6807\u628a\u5b83\u4eec\u62fc\u56de\u53bb\uff0c\u624d\u770b\u5230\u4e24\u6761\u9ad8\u8d28\u91cf\u8bb0\u5f55\u4e2d\u95f4\u5b8c\u6574\u7f3a\u5931\u4e86\u516d\u767e\u4e2a\u78b1\u57fa\u3002GraphAligner \u5b98\u65b9\u9879\u76ee<\/a><\/p>\n

\u4e00\u884c\u56fe\u6bd4\u5bf9\u540c\u65f6\u5305\u542b\u51e0\u5957\u4fe1\u606f<\/h2>\n

GAF \u7684\u524d\u51e0\u5217\u8bb0\u5f55\u67e5\u8be2\u540d\u79f0\u3001\u67e5\u8be2\u5168\u957f\u548c\u672c\u6761\u6bd4\u5bf9\u8986\u76d6\u7684\u67e5\u8be2\u8d77\u6b62\u4f4d\u7f6e\u3002\u518d\u5f80\u540e\u624d\u662f\u76ee\u6807\u8def\u5f84\uff0c\u5176\u4e2d\u7684\u8282\u70b9\u7f16\u53f7\u4e0e\u65b9\u5411\u63cf\u8ff0\u8fd9\u6bb5\u67e5\u8be2\u5728\u56fe\u4e0a\u7684\u8d70\u6cd5\u3002\u968f\u540e\u8fd8\u6709\u6bd4\u5bf9\u957f\u5ea6\u3001\u5339\u914d\u6570\u91cf\u4e0e\u6620\u5c04\u8d28\u91cf\u3002\u8868\u4e2d\u6bcf\u4e00\u884c\u8bc4\u4ef7\u7684\u662f\u8be5\u884c\u9009\u51fa\u7684\u5c40\u90e8\u5bf9\u5e94\u3002\u8d28\u91cf\u9ad8\u53ef\u4ee5\u8bf4\u660e\u8fd9\u6bb5\u4fa7\u7ffc\u5728\u7ed9\u5b9a\u56fe\u4e2d\u5b9a\u4f4d\u660e\u786e\uff0c\u5374\u4e0d\u4f1a\u66ff\u6ca1\u6709\u51fa\u73b0\u5728\u8fd9\u884c\u4e2d\u7684\u67e5\u8be2\u78b1\u57fa\u63d0\u4f9b\u8bc1\u636e\u3002\u60f3\u77e5\u9053\u4e00\u6761\u8bfb\u6bb5\u662f\u5426\u5b8c\u6574\u7a7f\u8fc7\u67d0\u4e2a\u6c14\u6ce1\uff0c\u5fc5\u987b\u8bfb\u53d6\u67e5\u8be2\u5750\u6807\uff0c\u800c\u4e0d\u80fd\u53ea\u7528\u6620\u5c04\u8d28\u91cf\u7b5b\u9009\u3002GAF \u5b57\u6bb5\u4e0e\u5750\u6807\u5b9a\u4e49<\/a><\/p>\n

\u8fd9\u91cc\u7684\u201c\u7a7f\u8fc7\u201d\u53ef\u4ee5\u76f4\u63a5\u5b9a\u4e49\u4e3a\u4e00\u6761\u6bd4\u5bf9\u8def\u5f84\u5305\u542b\u4e24\u4e2a\u5171\u4eab\u7684\u8fb9\u754c\u8282\u70b9\uff0c\u5e76\u4e14\u5728\u5b83\u4eec\u4e4b\u95f4\u6709\u6b63\u786e\u7684\u5185\u90e8\u8282\u70b9\u3002\u82e5\u8bfb\u6bb5\u53ea\u8986\u76d6\u5171\u4eab\u5de6\u7ffc\uff0c\u5373\u4f7f\u5b83\u4e0e\u5de6\u7ffc\u5e8f\u5217\u5168\u957f\u76f8\u540c\uff0c\u4e5f\u6ca1\u6709\u533a\u5206\u4e24\u6761\u5206\u652f\u7684\u78b1\u57fa\u3002\u4e00\u6761\u5b9e\u9a8c\u8bb0\u5f55\u81f3\u5c11\u8981\u5206\u522b\u8bf4\u660e\uff0c\u591a\u5c11\u5206\u5b50\u5230\u8fbe\u5de6\u8fb9\u754c\uff0c\u591a\u5c11\u5230\u8fbe\u53f3\u8fb9\u754c\uff0c\u591a\u5c11\u80fd\u7528\u540c\u4e00\u6761\u8fde\u7eed\u6bd4\u5bf9\u660e\u786e\u8fde\u63a5\u4e24\u4fa7\u3002\u4e09\u79cd\u8ba1\u6570\u53ef\u4ee5\u5b8c\u5168\u4e0d\u540c\uff0c\u6070\u597d\u76f8\u9047\u5728\u540c\u4e00\u4e2a\u5c40\u90e8\u533a\u57df\u4e5f\u4e0d\u80fd\u5408\u5e76\u6210\u4e00\u6761\u72ec\u7acb\u8de8\u8d8a\u8bc1\u636e\u3002<\/p>\n

\u5b9e\u8dd1\u7ecf\u9a8c\uff5c\u540c\u4e00\u6761\u8bfb\u6bb5\uff0c\u4e24\u5f20\u76ee\u6807\u56fe<\/h2>\n

\u6211\u4eec\u5b89\u88c5 GraphAligner 1.0.20\uff0c\u56fa\u5b9a\u968f\u673a\u79cd\u5b50\u751f\u6210\u5171\u4eab\u7684\u4e24\u4fa7\u8282\u70b9\uff0c\u5176\u4e2d\u5de6\u7ffc\u957f\u4e24\u5343\u4e8c\u767e\u78b1\u57fa\u3001\u53f3\u7ffc\u957f\u4e24\u5343\u4e09\u767e\u3002\u4e2d\u95f4\u5206\u522b\u653e\u4e24\u6761\u968f\u673a\u7684\u516d\u767e\u78b1\u57fa\u5e8f\u5217\u4f5c\u4e3a\u4e8c\u53f7\u3001\u4e09\u53f7\u5206\u652f\u3002\u6784\u9020\u4e24\u6761\u4e09\u5343\u4e94\u767e\u78b1\u57fa\u7684\u957f\u8bfb\u6bb5\uff0c\u5404\u7531\u5de6\u4fa7\u672b\u7aef\u4e00\u5343\u56db\u767e\u4e94\u5341\u78b1\u57fa\u3001\u76f8\u5e94\u5185\u90e8\u8282\u70b9\u548c\u53f3\u4fa7\u8d77\u59cb\u4e00\u5343\u56db\u767e\u4e94\u5341\u78b1\u57fa\u987a\u6b21\u7ec4\u6210\u3002\u7b2c\u4e09\u6761\u8bfb\u6bb5\u53ea\u53d6\u5171\u4eab\u5de6\u7ffc\uff0c\u4e13\u95e8\u4ee3\u8868\u65e0\u6cd5\u533a\u5206\u5206\u652f\u7684\u5bf9\u7167\u3002\u4e09\u6761\u8bfb\u6bb5\u90fd\u4fdd\u6301\u539f\u6837\uff0c\u8f6f\u4ef6\u91c7\u7528\u540c\u4e00\u4e2a\u9002\u7528\u4e8e\u53d8\u5f02\u56fe\u7684\u9884\u8bbe\u548c\u4e00\u4e2a\u7ebf\u7a0b\u3002<\/p>\n

\n\n\n\n\n\n\n\n\n
\u67e5\u8be2\u53ca\u76ee\u6807\u56fe<\/th>\n\u8fd4\u56de\u8def\u5f84<\/th>\n\u67e5\u8be2\u533a\u95f4<\/th>\n\u7f16\u8f91\u8ddd\u79bb\u548c MAPQ<\/th>\n<\/tr>\n<\/thead>\n
\u542b\u4e09\u53f7\u5206\u652f\u7684\u8bfb\u6bb5\uff0c\u5bf9\u5b8c\u6574\u56fe<\/td>\n1\u21923\u21924<\/td>\n[0,3499)<\/td>\n0\uff0c60<\/td>\n<\/tr>\n
\u540c\u4e00\u8bfb\u6bb5\uff0c\u5bf9\u5220\u9664\u4e09\u53f7\u5206\u652f\u7684\u56fe<\/td>\n1 \u548c 4 \u5404\u81ea\u4e00\u884c<\/td>\n[0,1450) \u548c [2050,3499)<\/td>\n\u4e24\u884c\u90fd\u662f 0\uff0c60<\/td>\n<\/tr>\n
\u542b\u4e8c\u53f7\u5206\u652f\u7684\u8bfb\u6bb5\uff0c\u5bf9\u4e24\u5f20\u56fe<\/td>\n\u5747\u4e3a 1\u21922\u21924<\/td>\n\u5747\u4e3a [0,3499)<\/td>\n\u90fd\u662f 0\uff0c60<\/td>\n<\/tr>\n
\u5171\u4eab\u5de6\u7ffc\u7684\u8bfb\u6bb5\uff0c\u5bf9\u4e24\u5f20\u56fe<\/td>\n\u5747\u53ea\u8d70\u8282\u70b9 1<\/td>\n\u5747\u4e3a [0,1498)<\/td>\n\u90fd\u662f 0\uff0c60<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n

\u5bf9\u7f3a\u5206\u652f\u7684\u56fe\uff0c\u4e24\u4e2a\u67e5\u8be2\u533a\u95f4\u7684\u5e76\u96c6\u957f\u5ea6\u662f\u4e00\u5343\u56db\u767e\u4e94\u5341\u52a0\u4e0a\u4e00\u5343\u56db\u767e\u56db\u5341\u4e5d\uff0c\u5171\u4e24\u5343\u516b\u767e\u4e5d\u5341\u4e5d\u78b1\u57fa\u3002\u5b8c\u6574\u56fe\u90a3\u4e00\u884c\u8986\u76d6\u4e09\u5343\u56db\u767e\u4e5d\u5341\u4e5d\u3002\u4e24\u6b21\u90fd\u628a\u672b\u7aef\u4e00\u4e2a\u78b1\u57fa\u7559\u5728\u6bd4\u5bf9\u4e4b\u5916\uff0c\u4e8c\u8005\u76f8\u51cf\u6b63\u597d\u662f\u516d\u767e\uff0c\u4e5f\u6b63\u597d\u662f\u8f93\u5165\u56fe\u4e2d\u5220\u53bb\u7684\u90a3\u6bb5\u3002\u6bcf\u4e2a\u4fa7\u7ffc\u90fd\u80fd\u6ca1\u6709\u9519\u914d\u5730\u627e\u5230\u5bf9\u5e94\uff0c\u6240\u4ee5\u4e24\u884c\u7684\u7f16\u8f91\u8ddd\u79bb\u540c\u65f6\u4e3a\u96f6\u5b8c\u5168\u7b26\u5408\u9884\u671f\u3002\u628a\u5c40\u90e8\u6bd4\u5bf9\u884c\u6570\u5f53\u6210\u6709\u6548\u8bfb\u6bb5\u6570\uff0c\u5374\u4f1a\u5f97\u5230\u8fd9\u4efd\u7f3a\u5206\u652f\u7684\u56fe\u652f\u6301\u53cd\u800c\u66f4\u591a\u7684\u9519\u8bef\u89e3\u8bfb\u3002<\/p>\n

\"\u4e24\u6761\u6ee1\u5206\u4fa7\u7ffc\uff0c\u7f3a\u4e86\u54ea\u4e00\u6bb5\u3002\u56fa\u5b9a\u4e00\u6761
\u56fa\u5b9a\u4e00\u6761 3500 bp \u6a21\u62df\u8bfb\u6bb5\uff0c\u6bd4\u8f83\u4e24\u5f20\u53ea\u76f8\u5dee\u4e00\u6761\u5206\u652f\u7684\u56fe\u3002<\/figcaption><\/figure>\n

\u4e3a\u4e86\u5f04\u6e05\u662f\u56fe\u53d8\u5316\u8fd8\u662f\u8f93\u5165\u8bfb\u6bb5\u53d1\u751f\u53d8\u5316\uff0c\u53ef\u4ee5\u50cf\u8fd9\u4e2a\u4f8b\u5b50\u4e00\u6837\u540c\u65f6\u4fdd\u7559\u4e24\u6761\u6027\u8d28\u4e0d\u540c\u7684\u5bf9\u7167\u3002\u4e00\u6761\u786e\u5b9e\u7a7f\u8fc7\u4ecd\u7136\u4fdd\u7559\u7684\u4e8c\u53f7\u652f\u8def\uff0c\u5e2e\u52a9\u53d1\u73b0\u8fd0\u884c\u53c2\u6570\u6216\u6587\u4ef6\u683c\u5f0f\u4e00\u5e76\u6539\u53d8\u7684\u95ee\u9898\u3002\u53e6\u4e00\u6761\u53ea\u5728\u5171\u4eab\u4fa7\u7ffc\u4e0a\uff0c\u63d0\u9192\u5206\u6790\u8005\u5373\u4f7f\u4e24\u5f20\u56fe\u7684\u8f93\u51fa\u5b8c\u5168\u76f8\u540c\uff0c\u5b83\u4e5f\u6ca1\u6709\u7ed9\u4efb\u4f55\u5185\u90e8\u7b49\u4f4d\u589e\u52a0\u652f\u6301\u3002\u771f\u5b9e\u9879\u76ee\u4e2d\u53ef\u4ee5\u4ece\u5df2\u77e5\u4f4d\u70b9\u6216\u5408\u6210\u5e8f\u5217\u6311\u9009\u76f8\u540c\u7c7b\u578b\u7684\u8bfb\u6bb5\uff0c\u5e76\u5728\u590d\u8dd1\u524d\u6838\u5bf9\u539f\u59cb\u8bfb\u6bb5\u6587\u4ef6\u6821\u9a8c\u503c\u3002<\/p>\n

\u82e5\u540e\u7eed\u8981\u6bd4\u8f83\u4e24\u79cd\u56fe\u7684\u6539\u8fdb\u6bd4\u4f8b\uff0c\u4ee5\u540c\u4e00\u7ec4\u539f\u59cb\u67e5\u8be2\u540d\u4e3a\u5206\u6bcd\u3002\u628a\u4ece\u5206\u6bb5\u53d8\u4e3a\u8fde\u7eed\u3001\u4ece\u8fde\u7eed\u9000\u56de\u5206\u6bb5\u3001\u4e24\u7248\u90fd\u8fde\u7eed\u3001\u4e24\u7248\u90fd\u672a\u5224\u5b9a\u5206\u5f00\u7edf\u8ba1\u3002\u8fd9\u6837\u624d\u770b\u5f97\u51fa\u6539\u8fdb\u6765\u81ea\u5bf9\u5df2\u6709\u8bfb\u6bb5\u7684\u89e3\u91ca\u80fd\u529b\uff0c\u8fd8\u662f\u6765\u81ea\u7eb3\u5165\u66f4\u591a\u539f\u672c\u8df3\u8fc7\u7684\u8bfb\u6bb5\u3002<\/p>\n

\u5982\u4f55\u628a\u7ed3\u679c\u6309\u4e00\u6761\u5206\u5b50\u91cd\u65b0\u8ba1\u7b97<\/h2>\n

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GraphAligner -g both.gfa -f reads.fa -a both.gaf -x vg -t 1\r\nGraphAligner -g omit3.gfa -f reads.fa -a omit3.gaf -x vg -t 1\r\nawk -F '\\t' '$1=="via3"{print $1,$2,$3,$4,$6,$10,$11,$12}' omit3.gaf\r\n<\/code><\/pre>\n
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