{"id":73321,"date":"2026-11-15T16:20:15","date_gmt":"2026-11-15T08:20:15","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=73321"},"modified":"2026-11-15T16:20:15","modified_gmt":"2026-11-15T08:20:15","slug":"pairtools-parse-dedup-distance-backend-phase-practice","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/pairtools-parse-dedup-distance-backend-phase-practice\/","title":{"rendered":"pairtools \u5b9e\u8dd1\u6307\u5357\u2014\u2014\u5750\u6807\u7ffb\u8f6c\u3001\u8d28\u91cf\u7b5b\u9009\u4e0e\u53bb\u91cd\u89c4\u5219\uff0c\u4e3a\u4ec0\u4e48\u540c\u4e00\u6279\u63a5\u89e6\u4f1a\u7559\u4e0b\u4e0d\u540c\u6570\u91cf"},"content":{"rendered":"<div class=\"ysx-method-guide\" style=\"max-width:820px;min-width:0;margin:0 auto;color:#26374a;line-height:1.86;overflow-wrap:anywhere\">\n<p>\u4e00\u4efd\u63a5\u89e6\u5217\u8868\u6362\u4e86\u53bb\u91cd\u53c2\u6570\uff0c\u4fdd\u7559\u6570\u91cf\u4ece\u56db\u6761\u53d8\u6210\u4e03\u6761\uff0c\u54ea\u4e2a\u7ed3\u679c\u624d\u6b63\u786e\uff1f\u5982\u679c\u6ca1\u6709\u5148\u5b9a\u4e49\u4ec0\u4e48\u7b97\u4f5c\u91cd\u590d\uff0c\u8fd9\u4e2a\u95ee\u9898\u6ca1\u6709\u552f\u4e00\u7b54\u6848\u3002\u4e24\u7aef\u5750\u6807\u5141\u8bb8\u504f\u79fb\u591a\u5c11\u3001\u4f7f\u7528\u6700\u5927\u504f\u79fb\u8fd8\u662f\u504f\u79fb\u4e4b\u548c\u3001\u90bb\u8fd1\u5173\u7cfb\u662f\u5426\u4f20\u9012\uff0c\u4ee5\u53ca\u662f\u5426\u8981\u6c42\u5355\u500d\u578b\u6807\u7b7e\u4e00\u81f4\uff0c\u90fd\u4f1a\u6539\u53d8\u91cd\u590d\u5206\u7ec4\u3002\u5b83\u4eec\u662f\u5206\u6790\u89c4\u5219\u7684\u4e00\u90e8\u5206\uff0c\u4e0d\u53ea\u662f\u8fd0\u884c\u901f\u5ea6\u9009\u9879\u3002<\/p>\n<p>\u672c\u6587\u5b89\u88c5\u5e76\u8fd0\u884c pairtools 1.1.3\uff0c\u7528\u5341\u4e8c\u5bf9\u624b\u5de5\u7f16\u5199\u7684\u6bd4\u5bf9\u8bb0\u5f55\u5b8c\u6210\u89e3\u6790\u3001\u6392\u5e8f\u3001\u7b5b\u9009\u548c\u4e94\u79cd\u53bb\u91cd\u5bf9\u7167\u3002\u8f93\u5165\u4e0d\u662f\u6d4b\u5e8f\u4eea\u4ea7\u751f\u7684\u6570\u636e\uff0c\u4e5f\u6ca1\u6709\u7ecf\u8fc7\u6bd4\u5bf9\u5668\uff0c\u56e0\u6b64\u672c\u6587\u8ba8\u8bba\u7684\u662f\u8f93\u5165\u8f93\u51fa\u8bed\u4e49\u4e0e\u53c2\u6570\u5f71\u54cd\uff0c\u4e0d\u662f\u6587\u5e93\u91cd\u590d\u7387\u3001\u771f\u5b9e\u751f\u7269\u5b66\u63a5\u89e6\u6216\u8f6f\u4ef6\u6027\u80fd\u6d4b\u8bc4\u3002<\/p>\n<figure class=\"guide-figure\" style=\"margin:24px 0 28px\"><img loading=\"lazy\" decoding=\"async\" src=\"\/wordpress\/wp-content\/uploads\/2026\/11\/pairtools-parse-dedup-distance-backend-phase-practice-guide.png\" alt=\"\u53bb\u91cd\u89c4\u5219\uff0c\u51b3\u5b9a\u4fdd\u7559\u4ec0\u4e48\u300212 \u5bf9\u4eba\u5de5\u6bd4\u5bf9\uff0c\u6bd4\u8f83\u8ddd\u79bb\u3001\u540e\u7aef\u4e0e\u5355\u500d\u578b\u6807\u7b7e\u3002\u8d28\u91cf\u95e8\u69db\u5148\u6539\u7c7b\u522b\uff0c\u63d0\u9ad8\u95e8\u69db\u540e\uff0c\u603b\u8bb0\u5f55\u4ecd\u662f 12 \u6761\uff0c\u663e\u5f0f\u7b5b\u9009 UU \u540e\uff0c\u53bb\u91cd\u8f93\u5165\u624d\u53d8\u6210 10 \u6761\u3002\u540e\u7aef\u4e5f\u6709\u8bed\u4e49\u5dee\u5f02\uff0c\u8fde\u7eed\u504f\u79fb\u94fe\u7684\u5206\u7ec4\u65b9\u5f0f\u4e0d\u540c\uff0c\u6700\u5927\u504f\u79fb\u4e09\u78b1\u57fa\uff0c\u672c\u4f8b\u4fdd\u7559 4 \u6761\u6216 5 \u6761\u3002\u6807\u7b7e\u4e0e\u7edf\u8ba1\u8981\u5206\u6e05\uff0c\u6807\u7b7e\u7ea6\u675f\u6539\u53d8\u91cd\u590d\u5206\u7ec4\uff0c\u7edf\u8ba1\u8fc7\u6ee4\u4e0d\u4f1a\u81ea\u52a8\u5220\u9664\u8f93\u51fa\u63a5\u89e6\u3002\" width=\"1200\" height=\"840\" style=\"display:block;width:100%;height:auto;border-radius:10px\"><figcaption style=\"font-size:14px;line-height:1.6;margin:9px 2px 0;color:#475569\">12 \u5bf9\u4eba\u5de5\u6bd4\u5bf9\uff0c\u6bd4\u8f83\u8ddd\u79bb\u3001\u540e\u7aef\u4e0e\u5355\u500d\u578b\u6807\u7b7e<\/figcaption><\/figure>\n<h2 style=\"font-size:1.38em;line-height:1.5;margin:1.55em 0 .55em;color:#182d43\">\u4e00\u3001\u5148\u628a\u8f93\u5165\u548c\u53ef\u56de\u7b54\u7684\u95ee\u9898\u9650\u5b9a\u6e05\u695a<\/h2>\n<p>\u5341\u4e8c\u5bf9\u8f93\u5165\u5305\u62ec\u4e09\u6761\u8fde\u7eed\u504f\u79fb\u7684\u63a5\u89e6\u3001\u4e00\u6761\u7cbe\u786e\u590d\u5236\u3001\u4e00\u6761\u4ea4\u6362\u6d4b\u5e8f\u7aef\u987a\u5e8f\u7684\u7b49\u4ef7\u63a5\u89e6\u3001\u4e00\u6761\u6539\u53d8\u65b9\u5411\u7684\u63a5\u89e6\u3001\u4e24\u6761\u7528\u4e8e\u6bd4\u8f83\u8ddd\u79bb\u89c4\u5219\u7684\u63a5\u89e6\u3001\u4e24\u6761\u5e26\u4e0d\u540c\u5355\u500d\u578b\u6807\u7b7e\u7684\u63a5\u89e6\u3001\u4e00\u6761\u4f4e\u6bd4\u5bf9\u8d28\u91cf\u63a5\u89e6\u548c\u4e00\u6761\u5b8c\u5168\u672a\u6bd4\u5bf9\u8bb0\u5f55\u3002\u6bcf\u79cd\u60c5\u51b5\u90fd\u6709\u660e\u786e\u8bbe\u8ba1\u76ee\u7684\uff0c\u80fd\u591f\u6cbf\u7740\u7a0b\u5e8f\u8f93\u51fa\u8ffd\u6eaf\u5230\u5bf9\u5e94\u8f93\u5165\u3002<\/p>\n<p>\u8bfb\u6bb5\u6309\u7167\u540d\u79f0\u6210\u7ec4\u653e\u7f6e\uff0c\u4f7f\u540c\u4e00\u5bf9\u7684\u4e24\u4e2a\u7aef\u76f8\u90bb\u3002\u672c\u6b21\u53ea\u6709\u7b80\u5355\u8fde\u7eed\u6bd4\u5bf9\uff0c\u6ca1\u6709\u8865\u5145\u6bd4\u5bf9\u548c\u591a\u91cd\u8fde\u63a5\u8def\u5f84\uff0c\u56e0\u6b64\u4e0d\u80fd\u501f\u8fd9\u4e2a\u4f8b\u5b50\u8bc4\u4ef7\u590d\u6742\u5d4c\u5408\u8bfb\u6bb5\u7684\u6062\u590d\u6548\u679c\u3002\u771f\u5b9e\u6570\u636e\u8fdb\u5165\u89e3\u6790\u9636\u6bb5\u65f6\uff0c\u9700\u8981\u786e\u4fdd\u540c\u4e00\u5206\u5b50\u7684\u76f8\u5173\u6bd4\u5bf9\u8bb0\u5f55\u6309\u5de5\u5177\u8981\u6c42\u7ec4\u7ec7\uff0c\u5426\u5219\u540e\u9762\u7684\u5206\u7c7b\u548c\u8fde\u63a5\u8bc6\u522b\u90fd\u5931\u53bb\u57fa\u7840\u3002<\/p>\n<p>\u56fa\u5b9a\u73af\u5883\u4e0e\u5b8c\u6574\u751f\u6210\u811a\u672c\u4fdd\u5b58\u5728<a style=\"color:#0e7490;text-decoration:underline;text-underline-offset:2px\" href=\"https:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2026\/11\/ysx-bioinformatics-practice-177-179-dc697a6dc10a.zip\">\u5b9e\u8dd1\u590d\u73b0\u5305<\/a>\u3002\u8fd0\u884c\u5668\u4f1a\u5efa\u7acb\u8f93\u5165\u5e76\u4f9d\u6b21\u6267\u884c\u5bf9\u7167\uff0c\u4e0d\u9700\u8981\u8bfb\u8005\u624b\u5de5\u5f55\u5165\u957f\u8868\u683c\u3002\u4e0b\u9762\u7684\u955c\u50cf\u6458\u8981\u56fa\u5b9a\u4e86\u672c\u6b21\u8fd0\u884c\u73af\u5883\uff0c\u4f7f\u7528\u53ef\u79fb\u52a8\u6807\u7b7e\u7684\u5176\u4ed6\u73af\u5883\u5e94\u91cd\u65b0\u6838\u5bf9\u7248\u672c\u3002<\/p>\n<pre style=\"max-width:100%;box-sizing:border-box;overflow-x:auto;margin:18px 0;padding:14px 16px;background:#f3f6fa;color:#1a293c;border:1px solid #d8e1ea;border-radius:8px;line-height:1.55;white-space:pre;overflow-wrap:normal;word-break:normal\"><code class=\"language-bash\">IMAGE=quay.io\/biocontainers\/pairtools@sha256:29e06e1791a809300c29abd8dea482eca573f2b9d0f8b8e2dddc0c749f561ba4\r\ndocker pull &quot;$IMAGE&quot;\r\npython3 run.py .\/pairtools_practice\r\n<\/code><\/pre>\n<p>pairtools \u7684\u4f18\u52bf\u662f\u628a\u63a5\u89e6\u5904\u7406\u62c6\u6210\u53ef\u7ec4\u5408\u6b65\u9aa4\uff0c\u65b9\u4fbf\u4fdd\u7559\u4e2d\u95f4\u7ed3\u679c\u548c\u5ba1\u8ba1\u8bb0\u5f55\u3002\u76f8\u5e94\u7684\u4f7f\u7528\u6210\u672c\u662f\uff0c\u89e3\u6790\u3001\u6392\u5e8f\u3001\u7b5b\u9009\u4e0e\u53bb\u91cd\u4e0d\u80fd\u88ab\u6df7\u4e3a\u4e00\u6b21\u201c\u6e05\u6d17\u201d\uff0c\u6bcf\u4e00\u6b65\u90fd\u9700\u8981\u77e5\u9053\u5176\u8f93\u5165\u72b6\u6001\u548c\u5b9e\u9645\u6539\u53d8\u4e86\u4ec0\u4e48\u3002<\/p>\n<h2 style=\"font-size:1.38em;line-height:1.5;margin:1.55em 0 .55em;color:#182d43\">\u4e8c\u3001\u63a5\u89e6\u4f4d\u7f6e\u8981\u7ed3\u5408\u65b9\u5411\u8bfb\uff0c\u4ea4\u6362\u6d4b\u5e8f\u7aef\u4e5f\u4e0d\u5e94\u589e\u52a0\u5206\u5b50\u6570<\/h2>\n<p>\u5728\u672c\u4f8b\u4e2d\uff0c\u4e00\u6761\u53cd\u5411\u4e94\u5341\u78b1\u57fa\u6bd4\u5bf9\u7684\u5de6\u4fa7\u8d77\u70b9\u4e3a\u4e5d\u767e\u4e94\u5341\u4e00\uff0c\u4e94\u7aef\u4f4d\u7f6e\u5728\u7b2c\u4e00\u5343\u4e2a\u78b1\u57fa\u3002\u8f93\u51fa\u63a5\u89e6\u4f4d\u7f6e\u91c7\u7528\u540e\u8005\u3002\u82e5\u76f4\u63a5\u628a\u6bd4\u5bf9\u6587\u4ef6\u7684\u8d77\u70b9\u590d\u5236\u8fdb\u63a5\u89e6\u8868\uff0c\u6b63\u5411\u8bb0\u5f55\u53ef\u80fd\u770b\u8d77\u6765\u6b63\u786e\uff0c\u53cd\u5411\u8bb0\u5f55\u5374\u53d1\u751f\u7cfb\u7edf\u6027\u504f\u79fb\uff0c\u968f\u540e\u57fa\u4e8e\u51e0\u4e2a\u78b1\u57fa\u5bb9\u5dee\u7684\u53bb\u91cd\u5c31\u4f1a\u53d7\u5230\u5f71\u54cd\u3002<\/p>\n<p>\u8fd9\u91cc\u7684\u63a5\u89e6\u4f4d\u7f6e\u662f\u4e00\u57fa\u5750\u6807\uff0c\u540e\u7eed\u8f6c\u6362\u6210\u5206\u7bb1\u65f6\u8981\u9075\u5b88\u76f8\u5e94\u63a5\u53e3\u7ea6\u5b9a\u3002\u4e0d\u8981\u770b\u5230\u67d0\u4e2a\u77e9\u9635\u683c\u5f0f\u4f7f\u7528\u96f6\u57fa\u533a\u95f4\uff0c\u5c31\u5728\u6240\u6709\u4e2d\u95f4\u6587\u4ef6\u91cc\u7edf\u4e00\u51cf\u4e00\u3002\u8f6c\u6362\u5e94\u8be5\u53d1\u751f\u5728\u660e\u786e\u7684\u63a5\u53e3\u4e0a\uff0c\u5e76\u901a\u8fc7\u8fb9\u754c\u4f4d\u7f6e\u7684\u5c0f\u4f8b\u5b50\u6838\u9a8c\u3002<\/p>\n<p>\u6211\u4eec\u8fd8\u7f16\u5199\u4e86\u4e00\u5bf9\u6d4b\u5e8f\u7aef\u987a\u5e8f\u4ea4\u6362\u7684\u8bb0\u5f55\u3002\u89e3\u6790\u65f6\u89c4\u8303\u5316\u4e24\u7aef\u987a\u5e8f\u540e\uff0c\u5b83\u548c\u539f\u59cb\u63a5\u89e6\u5177\u6709\u76f8\u540c\u5750\u6807\u4e0e\u65b9\u5411\u7ec4\u5408\uff0c\u80fd\u591f\u8fdb\u5165\u540c\u4e00\u4e2a\u91cd\u590d\u5206\u7ec4\u3002\u5173\u95ed\u7ffb\u8f6c\u7684\u5bf9\u7167\u5219\u4fdd\u7559\u539f\u6d4b\u5e8f\u7aef\u987a\u5e8f\u3002\u8fd9\u8bf4\u660e\u6392\u5e8f\u548c\u7ffb\u8f6c\u89e3\u51b3\u7684\u662f\u4e0d\u540c\u95ee\u9898\uff0c\u6392\u5e8f\u5b89\u6392\u8bb0\u5f55\u4e4b\u95f4\u7684\u6b21\u5e8f\uff0c\u7ffb\u8f6c\u89c4\u8303\u5316\u5355\u6761\u8bb0\u5f55\u4e24\u7aef\u7684\u8868\u793a\u3002<\/p>\n<p>\u5bf9\u4e8e\u67d3\u8272\u4f53\u95f4\u63a5\u89e6\uff0c\u89c4\u8303\u5316\u8fd8\u4f9d\u8d56\u67d3\u8272\u4f53\u6392\u5e8f\u89c4\u5219\u3002\u4e0d\u540c\u8f93\u5165\u6587\u4ef6\u5982\u679c\u91c7\u7528\u4e86\u4e0d\u540c\u53c2\u8003\u547d\u540d\u6216\u987a\u5e8f\uff0c\u5408\u5e76\u524d\u5e94\u8be5\u68c0\u67e5\u5934\u90e8\u4fe1\u606f\uff0c\u800c\u4e0d\u662f\u5220\u6389\u6240\u6709\u6ce8\u91ca\u884c\u540e\u76f4\u63a5\u62fc\u63a5\u3002\u6587\u4ef6\u5934\u91cc\u65e2\u6709\u5217\u5b9a\u4e49\uff0c\u4e5f\u6709\u5904\u7406\u5386\u53f2\uff0c\u4fdd\u7559\u5b83\u4eec\u6709\u52a9\u4e8e\u89e3\u91ca\u6570\u636e\u4ece\u54ea\u91cc\u6765\u3002<a style=\"color:#0e7490;text-decoration:underline;text-underline-offset:2px\" href=\"https:\/\/pairtools.readthedocs.io\/en\/latest\/formats.html\">\u5b98\u65b9\u683c\u5f0f\u6587\u6863<\/a>\u8bf4\u660e\u4e86\u5750\u6807\u3001\u4e24\u7aef\u8868\u793a\u548c\u63a5\u89e6\u7c7b\u578b\u7684\u7ea6\u5b9a\u3002<\/p>\n<h2 style=\"font-size:1.38em;line-height:1.5;margin:1.55em 0 .55em;color:#182d43\">\u4e09\u3001\u63d0\u9ad8\u6bd4\u5bf9\u8d28\u91cf\u95e8\u69db\uff0c\u5148\u6539\u53d8\u7684\u662f\u7c7b\u522b<\/h2>\n<p>\u672c\u6b21\u9ed8\u8ba4\u89e3\u6790\u5f97\u5230\u5341\u4e00\u6761\u4e24\u7aef\u552f\u4e00\u5b9a\u4f4d\u7c7b\u522b\uff0c\u4ee5\u53ca\u4e00\u6761\u5168\u672a\u6bd4\u5bf9\u7c7b\u522b\u3002\u628a\u6700\u5c0f\u6bd4\u5bf9\u8d28\u91cf\u6539\u4e3a\u4e09\u5341\u4e4b\u540e\uff0c\u5f97\u5230\u5341\u6761\u4e24\u7aef\u552f\u4e00\u5b9a\u4f4d\u3001\u4e00\u6761\u591a\u91cd\u6216\u4e0d\u6ee1\u8db3\u552f\u4e00\u5b9a\u4f4d\u95e8\u69db\u7684\u5355\u7aef\u4e0e\u552f\u4e00\u7aef\u7ec4\u5408\uff0c\u4ee5\u53ca\u4e00\u6761\u5168\u672a\u6bd4\u5bf9\u8bb0\u5f55\u3002\u603b\u8bb0\u5f55\u6570\u4ecd\u7136\u662f\u5341\u4e8c\u3002<\/p>\n<p>\u8fd9\u91cc\u7684\u201c\u552f\u4e00\u201d\u662f\u5de5\u5177\u7ed3\u5408\u5f53\u524d\u8d28\u91cf\u95e8\u69db\u4f5c\u51fa\u7684\u5206\u7c7b\uff0c\u4e0d\u5e94\u628a\u5b83\u5f53\u4f5c\u672a\u7ecf\u6761\u4ef6\u9650\u5b9a\u7684\u4e8b\u5b9e\u3002\u90a3\u6761\u5bf9\u7167\u8bb0\u5f55\u7684\u4e00\u7aef\u8d28\u91cf\u662f\u4e8c\u5341\u4e94\uff0c\u6539\u53d8\u95e8\u69db\u540e\u88ab\u91cd\u65b0\u5206\u7c7b\uff0c\u4e0d\u80fd\u8bf4\u5b83\u4ece\u6587\u4ef6\u4e2d\u81ea\u52a8\u6d88\u5931\u4e86\u3002<\/p>\n<pre style=\"max-width:100%;box-sizing:border-box;overflow-x:auto;margin:18px 0;padding:14px 16px;background:#f3f6fa;color:#1a293c;border:1px solid #d8e1ea;border-radius:8px;line-height:1.55;white-space:pre;overflow-wrap:normal;word-break:normal\"><code class=\"language-bash\">pairtools parse -c chrom.sizes \\\r\n  --min-mapq 30 --drop-sam --add-columns mapq,HP \\\r\n  -o q30.pairs toy.sam\r\n\r\npairtools sort --nproc 1 --memory 100M \\\r\n  -o sorted.pairs q30.pairs\r\n\r\npairtools select 'pair_type == &quot;UU&quot;' \\\r\n  -o uu.pairs sorted.pairs\r\n<\/code><\/pre>\n<p>\u6211\u4eec\u968f\u540e\u663e\u5f0f\u7b5b\u9009\u4e24\u7aef\u552f\u4e00\u5b9a\u4f4d\u7c7b\u522b\uff0c\u53bb\u91cd\u8f93\u5165\u624d\u53d8\u6210\u5341\u6761\u3002\u8fd9\u4e2a\u7b5b\u9009\u9002\u7528\u4e8e\u672c\u6587\u53ea\u6709\u7b80\u5355\u6bd4\u5bf9\u7684\u4eba\u5de5\u4f8b\u5b50\uff0c\u5e76\u4e0d\u662f\u6240\u6709\u771f\u5b9e Hi-C \u6570\u636e\u90fd\u5fc5\u987b\u53ea\u4fdd\u7559\u8fd9\u4e00\u7c7b\u3002\u590d\u6742\u8fde\u63a5\u6062\u590d\u53ef\u80fd\u4ea7\u751f\u5176\u4ed6\u53ef\u7528\u7c7b\u578b\uff0c\u6b63\u5f0f\u6d41\u7a0b\u5e94\u6839\u636e\u89e3\u6790\u7b56\u7565\u3001\u5b9e\u9a8c\u65b9\u6848\u548c\u7814\u7a76\u95ee\u9898\u786e\u5b9a\u63a5\u53d7\u96c6\u5408\u3002<\/p>\n<p>\u8fd9\u4e00\u6b65\u6700\u5b9e\u7528\u7684\u6838\u9a8c\u65b9\u6cd5\u662f\u540c\u65f6\u4fdd\u5b58\u89e3\u6790\u524d\u540e\u7684\u7c7b\u522b\u8ba1\u6570\uff0c\u4ee5\u53ca\u7b5b\u9009\u540e\u7684\u5b9e\u9645\u884c\u6570\u3002\u82e5\u4e00\u4efd\u62a5\u544a\u53ea\u7ed9\u51fa\u201c\u8fc7\u6ee4\u6389\u767e\u5206\u4e4b\u591a\u5c11\u201d\uff0c\u6ca1\u6709\u8bf4\u660e\u5206\u6bcd\u662f\u8bfb\u6bb5\u3001\u8bfb\u6bb5\u5bf9\u8fd8\u662f\u5df2\u89e3\u6790\u63a5\u89e6\uff0c\u5c31\u96be\u4ee5\u6bd4\u8f83\u4e0d\u540c\u6d41\u7a0b\u3002<\/p>\n<h2 style=\"font-size:1.38em;line-height:1.5;margin:1.55em 0 .55em;color:#182d43\">\u56db\u3001\u6700\u5927\u504f\u79fb\u4e0e\u504f\u79fb\u4e4b\u548c\uff0c\u662f\u4e24\u79cd\u4e0d\u540c\u91cd\u590d\u5b9a\u4e49<\/h2>\n<p>\u5148\u770b\u6211\u4eec\u7f16\u5199\u7684\u4e24\u6761\u63a5\u89e6\uff0c\u4e24\u7aef\u5750\u6807\u5206\u522b\u662f\u4e94\u5343\u548c\u4e03\u5343\uff0c\u4ee5\u53ca\u4e94\u5343\u96f6\u4e8c\u548c\u4e03\u5343\u96f6\u4e8c\u3002\u6bcf\u4e2a\u7aef\u90fd\u504f\u79fb\u4e24\u4e2a\u78b1\u57fa\u3002\u82e5\u4f7f\u7528\u6700\u5927\u7aef\u504f\u79fb\uff0c\u8ddd\u79bb\u662f\u4e8c\uff0c\u4e09\u78b1\u57fa\u95e8\u69db\u4e0b\u4f1a\u5408\u5e76\u3002\u82e5\u4f7f\u7528\u4e24\u7aef\u504f\u79fb\u4e4b\u548c\uff0c\u8ddd\u79bb\u662f\u56db\uff0c\u540c\u4e00\u95e8\u69db\u4e0b\u5c31\u4e0d\u4f1a\u5408\u5e76\u3002<\/p>\n<pre style=\"max-width:100%;box-sizing:border-box;overflow-x:auto;margin:18px 0;padding:14px 16px;background:#f3f6fa;color:#1a293c;border:1px solid #d8e1ea;border-radius:8px;line-height:1.55;white-space:pre;overflow-wrap:normal;word-break:normal\"><code class=\"language-bash\">pairtools dedup --backend scipy \\\r\n  --method max --max-mismatch 3 \\\r\n  --output dedup.pairs \\\r\n  --output-dups duplicates.pairs \\\r\n  --output-stats dedup.stats uu.pairs\r\n<\/code><\/pre>\n<div class=\"guide-table\" style=\"max-width:100%;overflow-x:auto;margin:18px 0\">\n<table style=\"display:table;width:100%;max-width:100%;min-width:0;table-layout:fixed;border-collapse:collapse;font-size:.92em;line-height:1.6\">\n<thead>\n<tr>\n<th scope=\"col\" style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;background:#eefbff;color:#1e293b;vertical-align:top;text-align:left;padding:6px;border:1px solid #c4cfdb\">\u672c\u6b21\u53bb\u91cd\u8bbe\u7f6e<\/th>\n<th scope=\"col\" style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;background:#eefbff;color:#1e293b;vertical-align:top;text-align:right;padding:6px;border:1px solid #c4cfdb\">\u4fdd\u7559\u63a5\u89e6<\/th>\n<th scope=\"col\" style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;background:#eefbff;color:#1e293b;vertical-align:top;text-align:right;padding:6px;border:1px solid #c4cfdb\">\u91cd\u590d\u63a5\u89e6<\/th>\n<th scope=\"col\" style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;background:#eefbff;color:#1e293b;vertical-align:top;text-align:left;padding:6px;border:1px solid #c4cfdb\">\u4e3b\u8981\u533a\u522b<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb\">\u6700\u5927\u7aef\u504f\u79fb\u4e09\u78b1\u57fa\uff0cscipy<\/td>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb;text-align:right\">4<\/td>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb;text-align:right\">6<\/td>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb\">\u90bb\u8fd1\u5173\u7cfb\u53ef\u4f20\u9012<\/td>\n<\/tr>\n<tr>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb\">\u6700\u5927\u7aef\u504f\u79fb\u4e09\u78b1\u57fa\uff0ccython<\/td>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb;text-align:right\">5<\/td>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb;text-align:right\">5<\/td>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb\">\u672c\u4f8b\u7684\u8fde\u7eed\u504f\u79fb\u94fe\u5206\u7ec4\u4e0d\u540c<\/td>\n<\/tr>\n<tr>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb\">\u4e24\u7aef\u504f\u79fb\u4e4b\u548c\u4e09\u78b1\u57fa\uff0cscipy<\/td>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb;text-align:right\">7<\/td>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb;text-align:right\">3<\/td>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb\">\u540c\u65f6\u504f\u79fb\u4e24\u7aef\u66f4\u96be\u5408\u5e76<\/td>\n<\/tr>\n<tr>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb\">\u5750\u6807\u5b8c\u5168\u4e00\u81f4\uff0cscipy<\/td>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb;text-align:right\">7<\/td>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb;text-align:right\">3<\/td>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb\">\u4e0d\u5141\u8bb8\u5750\u6807\u504f\u79fb<\/td>\n<\/tr>\n<tr>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb\">\u6700\u5927\u504f\u79fb\u4e09\u78b1\u57fa\u5e76\u8981\u6c42\u6807\u7b7e\u4e00\u81f4<\/td>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb;text-align:right\">5<\/td>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb;text-align:right\">5<\/td>\n<td style=\"white-space:normal;overflow-wrap:anywhere;word-break:normal;padding:6px;vertical-align:top;border:1px solid #c4cfdb\">\u4e0d\u540c\u5355\u500d\u578b\u6807\u7b7e\u5206\u522b\u4fdd\u7559<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n<p>\u8fd9\u5f20\u8868\u53ea\u80fd\u6bd4\u8f83\u672c\u6b21\u8bbe\u8ba1\u7684\u6570\u636e\uff0c\u4e0d\u80fd\u636e\u6b64\u5224\u65ad\u4fdd\u7559\u8d8a\u591a\u8d8a\u597d\uff0c\u4e5f\u4e0d\u80fd\u628a\u5220\u9664\u8d8a\u591a\u79f0\u4e3a\u53bb\u91cd\u8d8a\u5f7b\u5e95\u3002\u5bb9\u5dee\u653e\u5bbd\u53ef\u80fd\u5408\u5e76\u6280\u672f\u6027\u504f\u79fb\uff0c\u4e5f\u53ef\u80fd\u628a\u771f\u5b9e\u7684\u90bb\u8fd1\u72ec\u7acb\u5206\u5b50\u5408\u5728\u4e00\u8d77\u3002\u51b3\u5b9a\u89c4\u5219\u65f6\uff0c\u5e94\u7ed3\u5408\u6570\u636e\u4ea7\u751f\u65b9\u5f0f\u548c\u5df2\u6709\u6d41\u7a0b\u5b9a\u4e49\uff0c\u5e76\u628a\u9009\u62e9\u5199\u8fdb\u5206\u6790\u8bb0\u5f55\u3002<\/p>\n<p>\u4e24\u79cd\u89c4\u5219\u5728\u672c\u4f8b\u6070\u597d\u90fd\u7559\u4e0b\u4e03\u6761\uff0c\u4e5f\u4e0d\u8868\u793a\u5b83\u4eec\u5728\u4efb\u4f55\u6570\u636e\u4e0a\u7b49\u4ef7\u3002\u9047\u5230\u540c\u6837\u7684\u603b\u6570\uff0c\u4ecd\u7136\u8981\u6bd4\u8f83\u4fdd\u7559\u7684\u8bb0\u5f55\u8eab\u4efd\u53ca\u91cd\u590d\u5206\u7ec4\u3002\u7edf\u8ba1\u6570\u5b57\u76f8\u540c\u800c\u5177\u4f53\u5206\u5b50\u4e0d\u540c\uff0c\u4f1a\u7ed9\u4e0b\u6e38\u5c40\u90e8\u63a5\u89e6\u5206\u5e03\u5e26\u6765\u4e0d\u540c\u5f71\u54cd\u3002<\/p>\n<h2 style=\"font-size:1.38em;line-height:1.5;margin:1.55em 0 .55em;color:#182d43\">\u4e94\u3001\u8ba1\u7b97\u540e\u7aef\u4f1a\u6539\u53d8\u8fde\u7eed\u504f\u79fb\u94fe\u7684\u5904\u7406<\/h2>\n<p>\u6211\u4eec\u8fd8\u8bbe\u7f6e\u4e09\u6761\u63a5\u89e6\uff0c\u4e24\u7aef\u5750\u6807\u4f9d\u6b21\u4e3a\u4e00\u767e\u4e0e\u4e00\u5343\u3001\u4e00\u767e\u96f6\u4e09\u4e0e\u4e00\u5343\u96f6\u4e09\u3001\u4e00\u767e\u96f6\u516d\u4e0e\u4e00\u5343\u96f6\u516d\u3002\u7b2c\u4e00\u6761\u4e0e\u7b2c\u4e8c\u6761\u76f8\u5dee\u4e09\uff0c\u7b2c\u4e8c\u6761\u4e0e\u7b2c\u4e09\u6761\u4e5f\u76f8\u5dee\u4e09\uff0c\u4f46\u7b2c\u4e00\u6761\u4e0e\u7b2c\u4e09\u6761\u76f8\u5dee\u516d\u3002<\/p>\n<p>\u5728\u672c\u6b21 scipy \u540e\u7aef\u7684\u6700\u5927\u504f\u79fb\u4e09\u78b1\u57fa\u8bbe\u7f6e\u4e2d\uff0c\u8fd9\u4e09\u6761\u901a\u8fc7\u90bb\u8fd1\u5173\u7cfb\u8fde\u6210\u4e00\u4e2a\u91cd\u590d\u5206\u7ec4\u3002\u4f7f\u7528 cython \u540e\u7aef\u65f6\uff0c\u5206\u7ec4\u4e0d\u8981\u6c42\u8fd9\u79cd\u5173\u7cfb\u4f20\u9012\uff0c\u56e0\u6b64\u8be5\u94fe\u6700\u7ec8\u4fdd\u7559\u4e24\u6761\uff0c\u800c\u4e0d\u662f\u4e00\u6761\u3002\u7cbe\u786e\u590d\u5236\u548c\u4ea4\u6362\u6d4b\u5e8f\u7aef\u7684\u7b49\u4ef7\u8bb0\u5f55\u4ecd\u6309\u7167\u76f8\u5e94\u5750\u6807\u5f52\u5165\u91cd\u590d\u3002<\/p>\n<p>\u8fd9\u610f\u5473\u7740\u540e\u7aef\u4e0d\u80fd\u4e00\u6982\u89c6\u4e3a\u53ea\u6539\u53d8\u8fd0\u884c\u65f6\u95f4\u7684\u5b9e\u73b0\u7ec6\u8282\u3002\u5728\u9700\u8981\u5bf9\u7167\u65e7\u9879\u76ee\u65f6\uff0c\u9664\u4e86\u8f6f\u4ef6\u7248\u672c\u548c\u5bb9\u5dee\uff0c\u8fd8\u5e94\u8bb0\u5f55\u6240\u7528\u540e\u7aef\u3002\u82e5\u5347\u7ea7\u540e\u53d1\u73b0\u91cd\u590d\u7387\u53d8\u5316\uff0c\u5148\u7528\u8fd9\u79cd\u4e09\u6761\u63a5\u89e6\u7684\u5c0f\u4f8b\u5b50\u68c0\u67e5\u5b9a\u4e49\u5dee\u5f02\uff0c\u518d\u8ba8\u8bba\u662f\u5426\u662f\u539f\u59cb\u6570\u636e\u8d28\u91cf\u6539\u53d8\u3002<\/p>\n<p>\u5de5\u5177\u7684\u547d\u4ee4\u8bf4\u660e\u660e\u786e\u533a\u5206\u4e86\u8fd9\u4e9b\u540e\u7aef\u8bed\u4e49\u53ca\u8ddd\u79bb\u65b9\u6cd5\uff0c\u89c1<a style=\"color:#0e7490;text-decoration:underline;text-underline-offset:2px\" href=\"https:\/\/pairtools.readthedocs.io\/en\/latest\/cli_tools.html#pairtools-dedup\">\u5b98\u65b9\u547d\u4ee4\u63a5\u53e3<\/a>\u3002\u672c\u6587\u7684\u7ed3\u679c\u8fdb\u4e00\u6b65\u7ed9\u51fa\u4e00\u7ec4\u53ef\u4ee5\u6838\u5bf9\u7684\u8f93\u5165\uff0c\u800c\u4e0d\u662f\u4ec5\u628a\u6587\u6863\u4e2d\u7684\u9009\u9879\u540d\u79f0\u6284\u6210\u53c2\u6570\u63a8\u8350\u3002<\/p>\n<p>\u91cd\u590d\u5206\u7ec4\u8fd8\u6709\u4e00\u4e2a\u5bb9\u6613\u5ffd\u89c6\u7684\u89e3\u91ca\u8fb9\u754c\uff0c\u7559\u4e0b\u7684\u4ee3\u8868\u8bb0\u5f55\u4e0d\u81ea\u52a8\u7b49\u4e8e\u201c\u6d4b\u5e8f\u8d28\u91cf\u6700\u9ad8\u7684\u4e00\u6761\u201d\u3002\u5982\u679c\u4e0b\u6e38\u8981\u4f7f\u7528\u4ee3\u8868\u8bb0\u5f55\u643a\u5e26\u7684\u9644\u52a0\u5c5e\u6027\uff0c\u5e94\u6838\u5b9e\u5f53\u524d\u5904\u7406\u89c4\u5219\u5982\u4f55\u9009\u62e9\u4ee3\u8868\uff0c\u5e76\u68c0\u67e5\u8fd9\u4e9b\u5c5e\u6027\u662f\u5426\u9700\u8981\u5728\u5206\u7ec4\u5185\u5355\u72ec\u6c47\u603b\uff0c\u4e0d\u80fd\u51ed\u76f4\u89c9\u8d4b\u4e88\u4ee3\u8868\u884c\u989d\u5916\u542b\u4e49\u3002<\/p>\n<h2 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class=\"language-bash\">pairtools dedup --backend scipy \\\r\n  --method max --max-mismatch 3 \\\r\n  --extra-col-pair HP1 HP1 \\\r\n  --extra-col-pair HP2 HP2 \\\r\n  --output phased.pairs uu.pairs\r\n<\/code><\/pre>\n<p>\u8fd9\u4e2a\u4f8b\u5b50\u6f14\u793a\u7684\u662f\u9644\u52a0\u5217\u5982\u4f55\u53c2\u4e0e\u91cd\u590d\u5b9a\u4e49\uff0c\u4e0d\u8868\u793a\u52a0\u4e0a\u6807\u7b7e\u7ea6\u675f\u603b\u662f\u66f4\u5408\u7406\u3002\u771f\u5b9e\u5355\u500d\u578b\u6807\u7b7e\u53ef\u80fd\u7f3a\u5931\u6216\u5224\u65ad\u4e0d\u7a33\u5b9a\uff0c\u5982\u679c\u540c\u4e00\u4e2a\u6280\u672f\u91cd\u590d\u7684\u6807\u7b7e\u53d1\u751f\u5206\u6b67\uff0c\u5f3a\u5236\u6309\u6807\u7b7e\u5206\u7ec4\u4e5f\u53ef\u80fd\u628a\u672c\u5e94\u5408\u5e76\u7684\u8bb0\u5f55\u4fdd\u7559\u4e0b\u6765\u3002\u9009\u62e9\u524d\u5e94\u5148\u68c0\u67e5\u6807\u7b7e\u8d28\u91cf\u3001\u672a\u5b9a\u76f8\u6bd4\u4f8b\u548c\u6280\u672f\u91cd\u590d\u4e4b\u95f4\u7684\u4e00\u81f4\u6027\u3002<\/p>\n<p>\u6211\u4eec\u628a\u6807\u7b7e\u968f\u89e3\u6790\u7ed3\u679c\u4fdd\u7559\uff0c\u662f\u4e3a\u4e86\u8ba9\u8fd9\u4e2a\u5224\u65ad\u53ef\u4ee5\u5ba1\u8ba1\u3002\u82e5\u524d\u4e00\u6b65\u5df2\u7ecf\u5220\u9664\u4e86\u6807\u7b7e\u5217\uff0c\u540e\u9762\u518d\u5199\u6807\u7b7e\u7ea6\u675f\u547d\u4ee4\u4e5f\u65e0\u6cd5\u6062\u590d\u4fe1\u606f\u3002\u771f\u5b9e\u6d41\u7a0b\u8bbe\u8ba1\u5e94\u4ece\u6700\u7ec8\u5206\u6790\u9700\u8981\u53cd\u63a8\u4e2d\u95f4\u6587\u4ef6\u5fc5\u987b\u4fdd\u7559\u54ea\u4e9b\u5b57\u6bb5\uff0c\u540c\u65f6\u660e\u786e\u6bcf\u4e2a\u5b57\u6bb5\u7684\u7f3a\u5931\u503c\u8868\u793a\u3002<\/p>\n<p>\u65b9\u5411\u4fe1\u606f\u4e5f\u4e0d\u80fd\u5ffd\u7565\u3002\u672c\u6b21\u53e6\u5916\u7f16\u5199\u4e86\u4e00\u6761\u5750\u6807\u76f8\u540c\u4f46\u4e24\u7aef\u65b9\u5411\u7ec4\u5408\u4e0d\u540c\u7684\u63a5\u89e6\uff0c\u5b83\u5728\u5bf9\u7167\u4e2d\u5355\u72ec\u4fdd\u7559\u3002\u81ea\u884c\u7528\u4e24\u4e2a\u5750\u6807\u5217\u505a\u7b80\u5355\u53bb\u91cd\uff0c\u53ef\u80fd\u4e22\u6389\u5de5\u5177\u539f\u672c\u7528\u4e8e\u533a\u5206\u63a5\u89e6\u7684\u5b57\u6bb5\uff0c\u56e0\u6b64\u4e0d\u5b9c\u628a\u8fd9\u6837\u7684\u7b80\u5316\u811a\u672c\u5f53\u4f5c\u7b49\u4ef7\u66ff\u4ee3\u3002<\/p>\n<h2 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