{"id":70034,"date":"2026-11-14T22:53:54","date_gmt":"2026-11-14T14:53:54","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=70034"},"modified":"2026-11-14T22:53:54","modified_gmt":"2026-11-14T14:53:54","slug":"bwa-mem2-mapq-reference-duplicate-contig","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/bwa-mem2-mapq-reference-duplicate-contig\/","title":{"rendered":"BWA-MEM2 \u5b9e\u8dd1\uff5c\u540c\u4e00\u6761\u8bfb\u6bb5\u5206\u6beb\u672a\u6539\uff0c\u4e3a\u4ec0\u4e48 MAPQ \u4ece 0 \u5230\u4e86 60\uff1f"},"content":{"rendered":"
\n

\u9047\u5230\u4e24\u4e2a\u9879\u76ee\u7684\u6bd4\u5bf9\u8d28\u91cf\u5dee\u4e00\u622a\uff0c\u5f88\u591a\u4eba\u5148\u67e5\u6d4b\u5e8f\u8d28\u91cf\u6216\u6bd4\u5bf9\u53c2\u6570\u3002\u6709\u65f6\u7b54\u6848\u85cf\u5728\u53c2\u8003\u5e8f\u5217\u91cc\u3002\u6211\u4eec\u7ed9 BWA-MEM2 \u4e24\u6761\u5404\u957f\u4e24\u5343\u4e8c\u767e\u78b1\u57fa\u7684\u4eba\u5de5\u53c2\u8003\u5e8f\u5217\uff0c\u5176\u4e2d\u4e94\u767e\u78b1\u57fa\u5b8c\u5168\u76f8\u540c\u3002\u4ece\u5171\u4eab\u533a\u53d6\u4e00\u6761\u4e00\u767e\u78b1\u57fa\u7684\u8bfb\u6bb5\uff0c\u9762\u5bf9\u5b8c\u6574\u53c2\u8003\u65f6\uff0c\u5b83\u80fd\u5168\u957f\u5339\u914d\uff0c\u5b9a\u4f4d\u8d28\u91cf\u5374\u4e3a\u96f6\u3002\u53e6\u5efa\u4e00\u4efd\u7d22\u5f15\uff0c\u53ea\u4fdd\u7559\u7b2c\u4e00\u6761\u53c2\u8003\uff0c\u540c\u4e00\u6761\u8bfb\u6bb5\u4ee5\u540c\u6837\u7684\u5206\u6570\u5339\u914d\u5230\u540c\u4e00\u6bb5\u5e8f\u5217\uff0c\u5b9a\u4f4d\u8d28\u91cf\u5347\u5230\u516d\u5341\u3002\u4e0b\u9762\u7528\u53e6\u5916\u4e09\u6761\u5df2\u77e5\u6765\u6e90\u7684\u8bfb\u6bb5\u505a\u5bf9\u7167\uff0c\u5224\u65ad\u8fd9\u4e2a\u53d8\u5316\u7a76\u7adf\u80fd\u8bc1\u660e\u4ec0\u4e48\u3002<\/p>\n

\u6bd4\u5bf9\u5f97\u5206\u3001\u9519\u914d\u6570\u4e0e\u5b9a\u4f4d\u8d28\u91cf\u5206\u522b\u91cf\u4ec0\u4e48<\/h2>\n

\u8bfb\u53d6\u4e00\u884c SAM\uff0c\u5148\u628a\u4e09\u4e2a\u95ee\u9898\u5206\u5f00\u3002\u7b2c\u4e00\uff0c\u8fd9\u6bb5\u5e8f\u5217\u5728\u62a5\u544a\u7684\u4f4d\u7f6e\u4e0a\u6709\u591a\u543b\u5408\u3002\u7b2c\u4e8c\uff0c\u53c2\u8003\u4e2d\u662f\u5426\u8fd8\u6709\u63a5\u8fd1\u7684\u5019\u9009\u4f4d\u7f6e\u3002\u7b2c\u4e09\uff0c\u5199\u5728\u8f93\u51fa\u91cc\u7684\u8fd9\u6761\u8bb0\u5f55\u662f\u4e3b\u6bd4\u5bf9\u3001\u6b21\u8981\u6bd4\u5bf9\uff0c\u8fd8\u662f\u672a\u6bd4\u5bf9\u3002\u7b2c\u4e00\u9879\u53ef\u4ee5\u7ed3\u5408\u6bd4\u5bf9\u5f97\u5206\u3001\u7f16\u8f91\u8ddd\u79bb\u548c\u6bd4\u5bf9\u64cd\u4f5c\u68c0\u67e5\u3002\u7b2c\u4e8c\u9879\u9700\u8981\u7ed3\u5408\u5b9a\u4f4d\u8d28\u91cf\u3001\u5019\u9009\u5f97\u5206\u548c\u91cd\u590d\u533a\u80cc\u666f\u5224\u65ad\u3002\u7b2c\u4e09\u9879\u7531\u6807\u5fd7\u4f4d\u8bf4\u660e\u3002\u78b1\u57fa\u8d28\u91cf\u5219\u6765\u81ea\u6d4b\u5e8f\u73af\u8282\uff0c\u63cf\u8ff0\u5177\u4f53\u78b1\u57fa\u7684\u5224\u8bfb\u3002\u8fd9\u51e0\u9879\u90fd\u7528\u6570\u5b57\u8868\u793a\uff0c\u542b\u4e49\u548c\u9002\u7528\u7684\u4f4d\u7f6e\u5374\u5404\u81ea\u4e0d\u540c\u3002SAM \u683c\u5f0f\u89c4\u8303\u4e0e\u5b57\u6bb5\u5b9a\u4e49<\/a><\/p>\n

\u672c\u4f8b\u63a7\u5236\u539f\u59cb\u78b1\u57fa\u548c\u8d28\u91cf\u5b57\u7b26\u4e32\u59cb\u7ec8\u76f8\u540c\u3002\u6240\u6709\u67e5\u8be2\u90fd\u662f\u5355\u7aef\uff0c\u56fa\u5b9a\u4e00\u6761\u7ebf\u7a0b\uff0c\u540c\u65f6\u8981\u6c42\u62a5\u544a\u627e\u5230\u7684\u5176\u4ed6\u5355\u7aef\u6bd4\u5bf9\u3002\u8fd9\u6837\uff0c\u51fa\u73b0\u7b2c\u4e8c\u884c\u65f6\u80fd\u76f4\u63a5\u67e5\u770b\u5b83\u7684\u5750\u6807\u548c\u5f97\u5206\u3002\u9ed8\u8ba4\u8f93\u51fa\u53ea\u4fdd\u5b58\u90e8\u5206\u5019\u9009\u65f6\uff0c\u8868\u91cc\u5c11\u4e00\u884c\u5e76\u4e0d\u80fd\u8bc1\u660e\u53c2\u8003\u53ea\u5b58\u5728\u4e00\u4e2a\u543b\u5408\u4f4d\u7f6e\u3002\u5373\u4fbf\u6253\u5f00\u8fd9\u4e2a\u9009\u9879\uff0c\u542f\u53d1\u5f0f\u641c\u7d22\u4e5f\u6ca1\u6709\u7ed9\u51fa\u6240\u6709\u53ef\u80fd\u4f4d\u7f6e\u7684\u6570\u5b66\u679a\u4e3e\u3002\u5b9a\u4f4d\u8d28\u91cf\u662f\u5728\u5f53\u524d\u53c2\u8003\u548c\u8fd0\u884c\u6761\u4ef6\u4e0b\u5bf9\u5b9a\u4f4d\u6b67\u4e49\u7684\u4f30\u8ba1\uff0c\u53c2\u8003\u4e2d\u672a\u6536\u5f55\u7684\u5e8f\u5217\u81ea\u7136\u4e0d\u4f1a\u51fa\u73b0\u5728\u7ade\u4e89\u8005\u6e05\u5355\u91cc\u3002BWA-MEM2 \u4f5c\u8005\u7684\u5b89\u88c5\u4e0e\u8fd0\u884c\u8bf4\u660e<\/a><\/p>\n

\u5b9e\u8dd1\u7ecf\u9a8c\uff5c\u5171\u4eab\u533a\u5185\u90e8\u4e0e\u8de8\u8fb9\u754c\u8bfb\u6bb5\u7ed9\u51fa\u4e0d\u540c\u7b54\u6848<\/h2>\n

\u5b89\u88c5 BWA-MEM2 2.2.1 \u540e\uff0c\u6211\u4eec\u72ec\u7acb\u6784\u5efa\u53cc\u5e8f\u5217\u53c2\u8003\u4e0e\u5355\u5e8f\u5217\u53c2\u8003\u7684\u7d22\u5f15\u3002\u7b2c\u4e00\u6761\u8bfb\u6bb5\u5b8c\u5168\u843d\u5728\u5171\u4eab\u533a\uff0c\u7b2c\u4e8c\u3001\u7b2c\u4e09\u6761\u5206\u522b\u843d\u5728\u4e24\u6bb5\u72ec\u6709\u533a\u57df\uff0c\u7b2c\u56db\u6761\u8de8\u8d8a\u7b2c\u4e00\u6761\u53c2\u8003\u7684\u5171\u4eab\u533a\u8fb9\u754c\u3002\u4e3a\u4e86\u80fd\u7528\u7eb8\u7b14\u63a8\u7b97\u7ed3\u679c\uff0c\u53c2\u8003\u7531\u56fa\u5b9a\u968f\u673a\u79cd\u5b50\u6784\u9020\uff0c\u523b\u610f\u4fdd\u7559\u4e00\u4e2a\u8f83\u957f\u7684\u76f8\u540c\u7247\u6bb5\u3002\u5b9e\u9645\u6bd4\u5bf9\u90fd\u91cd\u65b0\u4ece\u540c\u4e00\u4efd FASTQ \u8bfb\u53d6\u56db\u6761\u67e5\u8be2\u3002\u4e0b\u8868\u4f4d\u7f6e\u6309 SAM \u7684\u4e00\u57fa\u5750\u6807\u89e3\u91ca\uff0c\u4e3b\u6bd4\u5bf9\u8868\u793a\u7a0b\u5e8f\u9009\u4f5c\u4e3b\u8981\u62a5\u544a\u7684\u8bb0\u5f55\u3002<\/p>\n

\n\n\n\n\n\n\n\n\n
\u8bfb\u6bb5<\/th>\n\u53c2\u8003\u540c\u65f6\u542b A\u3001B<\/th>\n\u53c2\u8003\u53ea\u542b A<\/th>\n<\/tr>\n<\/thead>\n
\u5b8c\u5168\u5728\u5171\u4eab\u533a<\/td>\nB \u7684 871 \u4f4d\u4e3a\u4e3b\uff0cA \u7684 871 \u4f4d\u4e3a\u6b21\uff0c\u4e24\u8005 MAPQ 0<\/td>\nA \u7684 871 \u4f4d\u4e3a\u4e3b\uff0cMAPQ 60<\/td>\n<\/tr>\n
A \u72ec\u6709\u533a<\/td>\nA \u7684 141 \u4f4d\uff0cMAPQ 60<\/td>\n\u540c\u4e00\u4f4d\u7f6e\uff0cMAPQ 60<\/td>\n<\/tr>\n
B \u72ec\u6709\u533a<\/td>\nB \u7684 141 \u4f4d\uff0cMAPQ 60<\/td>\n\u672a\u6bd4\u5bf9\uff0cFLAG 4<\/td>\n<\/tr>\n
A \u4e0e\u5171\u4eab\u533a\u4ea4\u754c<\/td>\nA \u4e0a\u5168\u957f\uff0c\u53e6\u6709 B \u4e0a 55 \u78b1\u57fa\u7684\u6b21\u6bd4\u5bf9<\/td>\nA \u4e0a\u5168\u957f\uff0cMAPQ 60<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\"\u4e00\u6761\u8bfb\u6bb5\uff0c\u4e24\u4efd\u53c2\u8003\u3002\u540c\u4e00\u6761
\u540c\u4e00\u6761 100 bp \u67e5\u8be2\uff0c\u4e24\u6b21\u6bd4\u5bf9\u78b1\u57fa\u548c\u8d28\u91cf\u503c\u5b8c\u5168\u76f8\u540c\u3002<\/figcaption><\/figure>\n

\u5728\u53cc\u5e8f\u5217\u53c2\u8003\u91cc\uff0c\u5171\u4eab\u533a\u8bfb\u6bb5\u4e24\u6761\u8bb0\u5f55\u7684\u6bd4\u5bf9\u5f97\u5206\u90fd\u4e3a\u4e00\u767e\uff0c\u7f16\u8f91\u8ddd\u79bb\u90fd\u4e3a\u96f6\uff0c\u4e3b\u8bb0\u5f55\u8fd8\u7ed9\u51fa\u4e86\u540c\u4e3a\u4e00\u767e\u7684\u6b21\u4f18\u5f97\u5206\u3002\u539f\u59cb\u5207\u7247\u5ba2\u89c2\u4e0a\u53d6\u81ea\u7b2c\u4e00\u6761\u53c2\u8003\uff0c\u672c\u6b21\u4e3b\u8bb0\u5f55\u504f\u504f\u5199\u5728\u7b2c\u4e8c\u6761\u3002\u7531\u4e8e\u4e24\u5904\u5e8f\u5217\u9010\u4e2a\u78b1\u57fa\u76f8\u540c\uff0c\u5355\u770b\u8fd9\u4e00\u767e\u4e2a\u78b1\u57fa\uff0c\u8bfb\u8005\u65e0\u4ece\u6062\u590d\u62bd\u6837\u65f6\u7684\u6807\u7b7e\u3002\u4e3b\u8bb0\u5f55\u5728\u8fd9\u91cc\u65b9\u4fbf\u4fdd\u5b58\u4e00\u4e2a\u4ee3\u8868\u4f4d\u7f6e\uff0c\u628a\u5b83\u5f53\u4f5c\u6765\u6e90\u9274\u5b9a\u4f1a\u4ea7\u751f\u9519\u8bef\u3002\u53bb\u6389\u7b2c\u4e8c\u6761\u53c2\u8003\u540e\uff0c\u4e3b\u8bb0\u5f55\u7684\u6bd4\u5bf9\u5f97\u5206\u4ecd\u4e3a\u4e00\u767e\uff0c\u6b21\u4f18\u5f97\u5206\u5b57\u6bb5\u53d8\u6210\u96f6\u3002\u8fd9\u4e00\u6b21\u589e\u52a0\u7684\u5b9a\u4f4d\u8d28\u91cf\u6765\u81ea\u53ef\u4f9b\u6bd4\u8f83\u7684\u4f4d\u7f6e\u53d8\u5c11\u3002<\/p>\n

\u8de8\u8fb9\u754c\u90a3\u6761\u8bfb\u6bb5\u63d0\u4f9b\u4e86\u66f4\u63a5\u8fd1\u5b9e\u9645\u8bca\u65ad\u7684\u4f8b\u5b50\u3002\u5b8c\u6574\u53c2\u8003\u4e2d\uff0c\u7b2c\u4e00\u6761\u53c2\u8003\u4e0a\u5f97\u5230\u4e00\u767e\u78b1\u57fa\u5168\u957f\u543b\u5408\uff0c\u5b9a\u4f4d\u8d28\u91cf\u516d\u5341\u3002\u7b2c\u4e8c\u6761\u4e0a\u53ea\u5bf9\u4e0a\u5171\u4eab\u90e8\u5206\u7684\u4e94\u5341\u4e94\u4e2a\u78b1\u57fa\uff0c\u6b21\u8bb0\u5f55\u7684\u64cd\u4f5c\u4e32\u4e3a 45H55M<\/code>\uff0c\u5f97\u5206\u4e94\u5341\u4e94\u3002\u8fd9\u91cc\u7684\u786c\u526a\u5207\u610f\u5473\u7740\u6b21\u8bb0\u5f55\u7684\u5e8f\u5217\u5b57\u6bb5\u4e0d\u5305\u542b\u88ab\u526a\u53bb\u7684\u56db\u5341\u4e94\u4e2a\u78b1\u57fa\uff0c\u539f\u59cb FASTQ \u4e2d\u5b83\u4eec\u4ecd\u7136\u5b58\u5728\u3002\u666e\u901a\u7684\u5339\u914d\u64cd\u4f5c\u7b26\u5141\u8bb8\u5339\u914d\u6216\u9519\u914d\uff0c\u8981\u786e\u8ba4\u8fd9\u4e2a\u4f8b\u5b50\u771f\u7684\u9010\u78b1\u57fa\u4e00\u81f4\uff0c\u8fd8\u5e94\u67e5\u770b\u7f16\u8f91\u8ddd\u79bb\u6216\u76f4\u63a5\u5bf9\u7167\u5e8f\u5217\u3002\u8de8\u51fa\u5171\u4eab\u533a\u7684\u90a3\u4e9b\u78b1\u57fa\u63d0\u4f9b\u4e86\u8db3\u4ee5\u533a\u5206\u4e24\u79cd\u4f4d\u7f6e\u7684\u4fe1\u606f\u3002BWA \u4f5c\u8005\u7684\u9009\u9879\u4e0e\u8f93\u51fa\u8bf4\u660e<\/a><\/p>\n

bwa-mem2 index both\/ref.fa\r\nbwa-mem2 index only_A\/ref.fa\r\nbwa-mem2 mem -t 1 -a both\/ref.fa query.fq > both.sam\r\nbwa-mem2 mem -t 1 -a only_A\/ref.fa query.fq > only_A.sam\r\nawk -F '\\t' '$1=="shared" || $1=="junctionA"' both.sam\r\n<\/code><\/pre>\n
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