{"id":71492,"date":"2026-11-15T01:08:37","date_gmt":"2026-11-14T17:08:37","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=71492"},"modified":"2026-11-15T01:15:02","modified_gmt":"2026-11-14T17:15:02","slug":"cactus-hal-liftover-interval-count-versus-base-coverage","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/cactus-hal-liftover-interval-count-versus-base-coverage\/","title":{"rendered":"Cactus \u7684 HAL \u6587\u4ef6\u600e\u4e48\u7528\uff5c\u540c\u4e00\u4e2a 55 bp \u533a\u95f4\u6295\u5f71\u540e\u8fd8\u6709\u8bb0\u5f55\uff0c\u4e3a\u4ec0\u4e48\u53ea\u627e\u56de 30 bp\uff1f"},"content":{"rendered":"
\n

\u628a\u4e00\u4e2a\u7269\u79cd\u7684\u8c03\u63a7\u533a\u6295\u5f71\u5230\u8fd1\u7f18\u7269\u79cd\uff0c\u5f97\u5230\u5750\u6807\u5c31\u7b97\u6210\u529f\u4e86\u5417\uff1f\u5982\u679c\u6307\u6807\u53ea\u5199\u201c\u6709\u7ed3\u679c\u7684\u533a\u95f4\u5360\u6bd4\u201d\uff0c\u4e00\u4e2a\u4e94\u5341\u4e94\u78b1\u57fa\u7684\u533a\u95f4\u4ec5\u5269\u4e24\u4fa7\u4e09\u5341\u4e2a\u78b1\u57fa\uff0c\u5b83\u4e5f\u53ef\u80fd\u88ab\u8ba1\u4e3a\u4e00\u6b21\u6210\u529f\u3002\u6211\u4eec\u7528 Cactus \u6b63\u5f0f\u53d1\u884c\u5305\u4e2d\u7684 HAL \u5de5\u5177\u6784\u9020\u4e24\u4efd\u5df2\u77e5\u7b54\u6848\u7684\u5168\u57fa\u56e0\u7ec4\u6bd4\u5bf9\uff0c\u5b9e\u9645\u505a\u6b63\u5411\u6295\u5f71\u548c\u53cd\u5411\u56de\u6295\u3002\u4e24\u4efd\u62a5\u544a\u90fd\u6709\u56db\u884c\u8f93\u51fa\uff0c\u4f46\u5176\u4e2d\u4e00\u4efd\u628a\u4e2d\u95f4\u7684\u4e00\u6bb5\u5b8c\u5168\u4e22\u6389\u4e86\u3002\u770b\u6e05\u8fd9\u4ef6\u4e8b\uff0c\u8981\u5728\u6bcf\u884c\u5750\u6807\u4e4b\u5916\u4fdd\u7559\u6e90\u533a\u95f4\u7684\u8eab\u4efd\u3002Cactus \u5b98\u65b9\u4f7f\u7528\u8bf4\u660e<\/a><\/p>\n

\u5bf9\u9f50\u6587\u4ef6\u80fd\u544a\u8bc9\u6211\u4eec\u54ea\u4e9b\u4e8b<\/h2>\n

Cactus \u53ef\u4ee5\u628a\u591a\u4e2a\u57fa\u56e0\u7ec4\u4e4b\u95f4\u7684\u5bf9\u5e94\u5173\u7cfb\u4fdd\u5b58\u5728 HAL \u6587\u4ef6\u4e2d\u3002\u7ed9\u5b9a\u6765\u6e90\u57fa\u56e0\u7ec4\u3001\u76ee\u6807\u57fa\u56e0\u7ec4\u548c\u6765\u6e90\u533a\u95f4\uff0c\u5de5\u5177\u6cbf\u73b0\u6709\u6bd4\u5bf9\u5bfb\u627e\u76f8\u5bf9\u5e94\u7684\u76ee\u6807\u4f4d\u7f6e\u3002\u8fd9\u79cd\u505a\u6cd5\u7684\u597d\u5904\u662f\u591a\u4e2a\u6837\u672c\u53ef\u4ee5\u5171\u4eab\u540c\u4e00\u5957\u6bd4\u5bf9\u5173\u7cfb\u3002\u9650\u5236\u4e5f\u6765\u81ea\u540c\u4e00\u4e2a\u5730\u65b9\uff0c\u8f93\u5165\u533a\u95f4\u4e2d\u54ea\u4e9b\u78b1\u57fa\u5728\u76ee\u6807\u91cc\u6709\u5bf9\u5e94\uff0c\u9700\u8981\u7531\u5df2\u6709\u6bd4\u5bf9\u652f\u6301\u3002\u4e00\u4e2a\u6765\u6e90\u533a\u95f4\u53ef\u80fd\u5bf9\u5e94\u591a\u4e2a\u76ee\u6807\u7247\u6bb5\uff0c\u4e00\u4e2a\u57fa\u56e0\u7ec4\u7684\u91cd\u590d\u62f7\u8d1d\u4e5f\u53ef\u80fd\u9020\u6210\u591a\u5904\u5339\u914d\uff0c\u4e0d\u80fd\u5148\u5047\u5b9a\u533a\u95f4\u4e00\u8fdb\u4e00\u51fa\u3002HAL \u9879\u76ee\u6587\u6863<\/a><\/p>\n

\u8bc4\u4f30\u524d\u6700\u597d\u5148\u9009\u5b9a\u5355\u4f4d\u3002\u82e5\u95ee\u9898\u662f\u201c\u8fd9\u4e2a\u57fa\u56e0\u9644\u8fd1\u6709\u6ca1\u6709\u4efb\u4f55\u53ef\u5bf9\u9f50\u5e8f\u5217\u201d\uff0c\u6709\u4e00\u4e2a\u77ed\u5339\u914d\u5c31\u53ef\u80fd\u503c\u5f97\u62a5\u544a\u3002\u82e5\u95ee\u9898\u662f\u201c\u5f15\u7269\u8986\u76d6\u7684\u7ed3\u5408\u4f4d\u70b9\u80fd\u5426\u5b8c\u6574\u5730\u8f6c\u5230\u53e6\u4e00\u4efd\u7ec4\u88c5\u201d\uff0c\u4e24\u7aef\u4e4b\u95f4\u6bcf\u4e2a\u5173\u952e\u78b1\u57fa\u7684\u5bf9\u5e94\u90fd\u5f88\u91cd\u8981\u3002\u82e5\u95ee\u9898\u662f\u201c\u540c\u4e00\u6bb5\u5e8f\u5217\u5728\u53e6\u4e00\u4e2a\u57fa\u56e0\u7ec4\u662f\u5426\u53ea\u6709\u4e00\u4efd\u201d\uff0c\u8fd8\u8981\u7edf\u8ba1\u53bb\u91cd\u540e\u547d\u4e2d\u51e0\u4e2a\u4e0d\u540c\u4f4d\u7f6e\u3002\u4e09\u7c7b\u7ed3\u679c\u90fd\u80fd\u4ece\u5750\u6807\u8868\u5165\u624b\uff0c\u4f46\u4e0d\u80fd\u628a\u8f93\u51fa\u884c\u6570\u76f4\u63a5\u586b\u5165\u540c\u4e00\u4e2a\u6210\u529f\u7387\u680f\u3002<\/p>\n

\u5b9e\u8dd1\u7ecf\u9a8c\uff5c\u7ed9\u76ee\u6807\u6bd4\u5bf9\u7559\u4e00\u6bb5\u6070\u597d 25 bp \u7684\u7f3a\u53e3<\/h2>\n

\u6211\u4eec\u53d6\u4e09\u767e\u78b1\u57fa\u7684\u4eba\u5de5\u53c2\u8003\uff0c\u8bbe\u7f6e\u4e24\u4e2a\u5bf9\u7167\u3002\u7b2c\u4e00\u4e2a\u76ee\u6807\u4e0e\u53c2\u8003\u5b8c\u5168\u76f8\u540c\u3002\u7b2c\u4e8c\u4e2a\u76ee\u6807\u7701\u53bb\u539f\u6765\u4ece\u96f6\u5f00\u59cb\u8ba1\u6570\u7684\u7b2c\u4e00\u767e\u81f3\u7b2c\u4e00\u767e\u4e8c\u5341\u4e94\u4e4b\u95f4\u7684\u4e8c\u5341\u4e94\u4e2a\u78b1\u57fa\uff0c\u4f59\u4e0b\u78b1\u57fa\u4ecd\u6309\u539f\u987a\u5e8f\u76f8\u8fde\u3002\u7528\u8fd9\u4e24\u4e2a\u5df2\u77e5\u7684\u6210\u5bf9\u6bd4\u5bf9\u5206\u522b\u751f\u6210 HAL\uff0c\u518d\u8c03\u7528\u53d1\u884c\u5305\u4e2d\u7684\u6b63\u5411\u548c\u53cd\u5411\u5750\u6807\u6295\u5f71\u3002\u5b9e\u9645\u5b89\u88c5\u7684\u662f Cactus 4.0.0 \u53d1\u884c\u5305\uff0c\u672c\u6b21\u8fd0\u884c\u5176\u9644\u5e26\u7684 HAL 2.2 \u5de5\u5177\u3002\u56e0\u4e3a\u5e0c\u671b\u63d0\u524d\u77e5\u9053\u6bcf\u4e00\u4e2a\u5bf9\u9f50\u5217\u7684\u6b63\u786e\u5bf9\u5e94\uff0c\u8f93\u5165\u4ece\u6784\u9020\u597d\u7684\u6bd4\u5bf9\u8d77\u6b65\uff0c\u6ca1\u6709\u8ba9 Cactus \u91cd\u65b0\u63a8\u65ad\u6574\u5957\u591a\u57fa\u56e0\u7ec4\u6bd4\u5bf9\u3002<\/p>\n

\u6211\u4eec\u9001\u5165\u56db\u6761\u5e26\u552f\u4e00\u540d\u79f0\u7684\u534a\u5f00\u533a\u95f4\u3002\u4e00\u6761\u6a2a\u8de8\u6574\u6bb5\u5dee\u5f02\uff0c\u4e09\u6761\u5206\u522b\u4f4d\u4e8e\u5b83\u7684\u5de6\u4fa7\u3001\u4e2d\u95f4\u548c\u53f3\u4fa7\u3002\u4ee5\u4ece\u96f6\u8ba1\u6570\u3001\u5de6\u7aef\u5305\u542b\u5e76\u6392\u9664\u53f3\u7aef\u7684\u89c4\u5219\u4e66\u5199\uff0c\u533a\u95f4\u957f\u5ea6\u5c31\u662f\u53f3\u7aef\u51cf\u5de6\u7aef\u3002\u7b2c\u56db\u5217\u540d\u79f0\u8ba9\u8de8\u8d8a\u533a\u95f4\u7684\u4e24\u884c\u8f93\u51fa\u53ef\u4ee5\u91cd\u65b0\u805a\u5230\u4e00\u8d77\uff0c\u4e5f\u9632\u6b62\u51e0\u6761\u5750\u6807\u90e8\u5206\u91cd\u53e0\u7684\u6d4b\u8bd5\u8bb0\u5f55\u5728\u7edf\u8ba1\u65f6\u88ab\u8bef\u8ba4\u4f5c\u540c\u4e00\u6761\u3002UCSC \u5bf9 BED \u5750\u6807\u7684\u5b9a\u4e49<\/a><\/p>\n

\n\n\n\n\n\n\n\n\n
\u6e90\u533a\u95f4<\/th>\n\u5b8c\u5168\u76f8\u540c\u7684\u76ee\u6807<\/th>\n\u76ee\u6807\u5c11 25 bp \u65f6\u7684\u8f93\u51fa<\/th>\n\u56de\u5230\u6e90\u5750\u6807\u540e\u8986\u76d6<\/th>\n<\/tr>\n<\/thead>\n
\u8de8\u8d8a [90,145)<\/td>\n[90,145)<\/td>\n[90,100) \u4e0e [100,120)<\/td>\n30 \/ 55 bp<\/td>\n<\/tr>\n
\u5de6\u4fa7 [90,100)<\/td>\n[90,100)<\/td>\n[90,100)<\/td>\n10 \/ 10 bp<\/td>\n<\/tr>\n
\u4e2d\u95f4 [100,125)<\/td>\n[100,125)<\/td>\n\u65e0\u5bf9\u5e94\u8bb0\u5f55<\/td>\n0 \/ 25 bp<\/td>\n<\/tr>\n
\u53f3\u4fa7 [125,145)<\/td>\n[125,145)<\/td>\n[100,120)<\/td>\n20 \/ 20 bp<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n

\u7b2c\u4e8c\u4e2a\u76ee\u6807\u4e0a\uff0c\u8de8\u8d8a\u533a\u95f4\u5f97\u5230\u7684\u4e24\u6bb5\u521a\u597d\u76f8\u90bb\u3002\u82e5\u7acb\u523b\u628a\u76f8\u90bb\u7247\u6bb5\u5408\u5e76\uff0c\u5b83\u4eec\u4f1a\u6210\u4e3a\u4e00\u6761\u8fde\u7eed\u4e09\u5341\u78b1\u57fa\u7684\u76ee\u6807\u8bb0\u5f55\u3002\u968f\u540e\u6cbf\u540c\u4e00\u4efd\u6bd4\u5bf9\u56de\u5230\u6e90\u57fa\u56e0\u7ec4\uff0c\u4e24\u6bb5\u5206\u522b\u843d\u5728\u539f\u59cb\u7684\u4e5d\u5341\u5230\u4e00\u767e\uff0c\u4ee5\u53ca\u4e00\u767e\u4e8c\u5341\u4e94\u5230\u4e00\u767e\u56db\u5341\u4e94\uff0c\u6b63\u4e2d\u95f4\u6ca1\u6709\u56de\u6765\u3002\u82e5\u4e3a\u56de\u6295\u7ed3\u679c\u53ea\u8bb0\u6700\u5c0f\u8d77\u70b9\u548c\u6700\u5927\u7ec8\u70b9\uff0c\u5f97\u5230\u7684\u5916\u5305\u533a\u95f4\u53c8\u4f1a\u957f\u8fbe\u4e94\u5341\u4e94\u4e2a\u78b1\u57fa\uff0c\u8db3\u4ee5\u9020\u6210\u5b8c\u6574\u8f6c\u79fb\u7684\u9519\u89c9\u3002\u8981\u8ba1\u7b97\u5b9e\u9645\u8986\u76d6\uff0c\u5e94\u53d6\u56de\u6295\u533a\u95f4\u7684\u5e76\u96c6\u540e\u6c42\u957f\u5ea6\uff0c\u4fdd\u7559\u5185\u90e8\u7a7a\u6863\u3002<\/p>\n

\"55
\u76ee\u6807\u5c11 25 \u4e2a\u78b1\u57fa\u540e\uff0c\u56db\u6761\u8f93\u5165\u4ecd\u80fd\u4ea7\u751f\u56db\u884c\u8f93\u51fa\u3002<\/figcaption><\/figure>\n
maf2hal --refGenome ref known.maf known.hal\r\nhalStats --genomes known.hal\r\nhalLiftover known.hal ref source.bed alt target.bed\r\nhalLiftover known.hal alt target.bed ref back.bed\r\n<\/code><\/pre>\n
\u5bf9\u5df2\u6709\u6ce8\u91ca\u8fd8\u8981\u6ce8\u610f\u8bb0\u5f55\u5c42\u7ea7\u3002\u4e00\u4e2a\u57fa\u56e0\u7684\u4e0d\u540c\u5916\u663e\u5b50\u53ef\u80fd\u5206\u5e03\u5728\u76f8\u8ddd\u5f88\u8fdc\u7684\u533a\u95f4\uff0c\u53ea\u7528\u6574\u6761\u57fa\u56e0\u7684\u8d77\u6b62\u6295\u5f71\uff0c\u4f1a\u628a\u539f\u672c\u4e0d\u5c5e\u4e8e\u5916\u663e\u5b50\u7684\u78b1\u57fa\u7b97\u8fdb\u53bb\u3002\u628a\u5916\u663e\u5b50\u5206\u522b\u5e26\u4e0a\u7a33\u5b9a\u7f16\u53f7\u6295\u5f71\uff0c\u518d\u6309\u94fe\u65b9\u5411\u91cd\u5efa\u8f6c\u5f55\u672c\u987a\u5e8f\u3002\u6b64\u65f6\u80fd\u591f\u56de\u7b54\u7684\u662f\u7f16\u7801\u533a\u54ea\u4e9b\u78b1\u57fa\u6709\u5bf9\u5e94\u3001\u8fb9\u754c\u662f\u5426\u4fdd\u7559\uff0c\u4ee5\u53ca\u54ea\u4e00\u4e2a\u5916\u663e\u5b50\u5148\u51fa\u73b0\u65ad\u70b9\uff0c\u8fd9\u6bd4\u53ea\u6bd4\u8f83\u57fa\u56e0\u4e24\u7aef\u5750\u6807\u66f4\u63a5\u8fd1\u529f\u80fd\u5224\u65ad\u6240\u9700\u7684\u8bc1\u636e\u3002<\/p>\n
\u5982\u4f55\u4ece\u4e00\u4e2a\u6210\u529f\u7387\u8fd8\u539f\u6210\u80fd\u7528\u7684\u7ed3\u679c<\/h2>\n
\u672c\u4f8b\u4e24\u4efd\u6b63\u5411\u6587\u4ef6\u6070\u597d\u90fd\u6709\u56db\u884c\u3002\u7b2c\u4e00\u4e2a\u5bf9\u7167\u662f\u56db\u4e2a\u6765\u6e90\u6807\u7b7e\u5404\u51fa\u4e00\u884c\uff0c\u53e6\u4e00\u4e2a\u662f\u4e09\u4e2a\u6765\u6e90\u6807\u7b7e\u6709\u7ed3\u679c\uff0c\u5176\u4e2d\u8de8\u8d8a\u6807\u7b7e\u51fa\u4e24\u884c\uff0c\u4e2d\u95f4\u6807\u7b7e\u96f6\u884c\u3002\u68c0\u67e5\u539f\u59cb\u6e05\u5355\u65f6\u4e00\u5b9a\u628a\u672a\u51fa\u73b0\u5728\u8f93\u51fa\u4e2d\u7684\u6807\u7b7e\u8865\u56de\uff0c\u6309\u539f\u59cb\u8bb0\u5f55\u7ed9\u5b83\u7684\u8986\u76d6\u586b\u96f6\u3002\u53ea\u4ece\u8f93\u51fa\u6587\u4ef6\u5206\u7ec4\uff0c\u7f3a\u5931\u6700\u5f7b\u5e95\u7684\u90a3\u4e00\u6761\u53cd\u800c\u4e0d\u4f1a\u8fdb\u5165\u8bc4\u4ef7\u3002\u4e24\u4e2a\u76ee\u6807\u5373\u4f7f\u62e5\u6709\u76f8\u540c\u884c\u6570\uff0c\u5728\u201c\u6709\u4efb\u610f\u6620\u5c04\u7684\u7279\u5f81\u6570\u201d\u548c\u201c\u5b8c\u6574\u6620\u5c04\u7684\u7279\u5f81\u6570\u201d\u4e0a\u90fd\u4e0d\u76f8\u540c\u3002<\/p>\n
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