{"id":70099,"date":"2026-11-14T23:04:57","date_gmt":"2026-11-14T15:04:57","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=70099"},"modified":"2026-11-14T23:04:57","modified_gmt":"2026-11-14T15:04:57","slug":"picard-markduplicates-read-groups-library-id","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/picard-markduplicates-read-groups-library-id\/","title":{"rendered":"Picard \u5b9e\u8dd1\uff5c\u4e24\u5bf9\u8bfb\u6bb5\u8d77\u6b62\u4f4d\u7f6e\u5b8c\u5168\u76f8\u540c\uff0c\u4e3a\u4ec0\u4e48\u6362\u4e00\u9879\u6587\u5e93\u4fe1\u606f\u5c31\u4e0d\u518d\u6807\u91cd\u590d\uff1f"},"content":{"rendered":"
\n

\u4e24\u4e2a\u6d4b\u5e8f\u6587\u4ef6\u5408\u5e76\u540e\uff0c\u91cd\u590d\u7387\u7a81\u7136\u5347\u9ad8\uff0c\u5e38\u89c1\u7684\u6392\u67e5\u52a8\u4f5c\u662f\u56de\u5934\u770b\u5efa\u5e93\u91cf\u548c\u6269\u589e\u8f6e\u6570\u3002\u8fd8\u6709\u4e00\u4e2a\u51e0\u4e4e\u4e0d\u82b1\u65f6\u95f4\u7684\u68c0\u67e5\uff0c\u6253\u5f00 BAM \u5934\uff0c\u6838\u5bf9\u4e24\u4e2a\u8bfb\u7ec4\u5199\u7684\u662f\u540c\u4e00\u4efd\u6587\u5e93\uff0c\u8fd8\u662f\u4e24\u4efd\u72ec\u7acb\u6587\u5e93\u3002\u6211\u4eec\u7528 Picard \u5bf9\u540c\u6837\u7684\u4e09\u5bf9\u8bfb\u6bb5\u505a\u4e86\u4e24\u6b21\u6807\u8bb0\uff0c\u6837\u672c\u540d\u3001\u8bfb\u7ec4\u540d\u3001\u5750\u6807\u3001\u65b9\u5411\u548c\u78b1\u57fa\u8d28\u91cf\u90fd\u6ca1\u6539\uff0c\u53ea\u6539\u7b2c\u4e8c\u4e2a\u8bfb\u7ec4\u7684\u6587\u5e93\u6807\u8bc6\u3002\u7b2c\u4e00\u6b21\u6709\u4e00\u5bf9\u88ab\u6807\u91cd\u590d\uff0c\u7b2c\u4e8c\u6b21\u4e00\u5bf9\u4e5f\u6ca1\u6709\u3002\u7406\u89e3\u8fd9\u4e2a\u5dee\u5f02\uff0c\u6709\u52a9\u4e8e\u5224\u65ad\u5408\u5e76\u6cf3\u9053\u3001\u5408\u5e76\u6587\u5e93\u4ee5\u53ca\u8ba1\u7b97\u6709\u6548\u6df1\u5ea6\u65f6\u8be5\u4fdd\u7559\u54ea\u4e9b\u4fe1\u606f\u3002<\/p>\n

\u4ece\u5b9e\u9a8c\u8bb0\u5f55\u8ffd\u5230 BAM \u6587\u4ef6\u5934\u7684\u4e09\u4e2a\u5b57\u6bb5<\/h2>\n

\u6837\u672c\u6807\u8bc6\u56de\u7b54\u8fd9\u4e9b\u6570\u636e\u5c5e\u4e8e\u8c01\u3002\u6587\u5e93\u6807\u8bc6\u56de\u7b54\u5b83\u4eec\u7531\u54ea\u4e00\u6b21\u5efa\u5e93\u5f97\u5230\u3002\u8bfb\u7ec4\u6807\u8bc6\u5219\u8ba9\u6bcf\u6761\u6bd4\u5bf9\u8bb0\u5f55\u80fd\u6307\u56de\u6587\u4ef6\u5934\u7684\u4e00\u6761\u8bfb\u7ec4\u58f0\u660e\u3002\u4e00\u4e2a\u6837\u672c\u53ef\u4ee5\u72ec\u7acb\u5efa\u4e24\u4efd\u6587\u5e93\uff0c\u4e00\u4efd\u6587\u5e93\u4e5f\u53ef\u4ee5\u5206\u5230\u4e0d\u540c\u6cf3\u9053\u6d4b\u5e8f\u3002\u5408\u5e76\u6587\u4ef6\u540e\uff0c\u53ea\u4fdd\u7559\u76f8\u540c\u6837\u672c\u540d\u65e0\u6cd5\u6062\u590d\u8fd9\u4e9b\u5b9e\u9a8c\u5173\u7cfb\u3002\u5e94\u4ece\u5b9e\u9a8c\u8bb0\u5f55\u6574\u7406\u6837\u672c\u3001\u5efa\u5e93\u6279\u6b21\u3001\u6cf3\u9053\u7684\u5bf9\u5e94\uff0c\u518d\u68c0\u67e5\u6bcf\u6761\u8bb0\u5f55\u4e0a\u7684\u8bfb\u7ec4\u6807\u8bb0\u80fd\u5426\u5728\u6587\u4ef6\u5934\u627e\u5230\uff0c\u5934\u91cc\u7684\u6587\u5e93\u5b57\u6bb5\u6709\u6ca1\u6709\u6b63\u786e\u586b\u5199\u3002SAM \u89c4\u8303\u4e2d\u7684\u8bfb\u7ec4\u4e0e\u6587\u5e93\u5b57\u6bb5<\/a><\/p>\n

Picard \u7684\u4f4d\u7f6e\u6cd5\u4f1a\u7ed3\u5408\u6587\u5e93\u4fe1\u606f\u4e0e\u8bfb\u6bb5\u7684\u65b9\u5411\u3001\u672a\u526a\u5207\u7684\u4e94\u7aef\u4f4d\u7f6e\u7b49\u7279\u5f81\u5bfb\u627e\u91cd\u590d\u5019\u9009\u3002\u6570\u636e\u662f\u6210\u5bf9\u8fd8\u662f\u5355\u7aef\uff0c\u4e5f\u4f1a\u5f71\u54cd\u5b83\u80fd\u5229\u7528\u7684\u4fe1\u606f\u3002\u9ed8\u8ba4\u8bc4\u5206\u7b56\u7565\u4f1a\u5229\u7528\u78b1\u57fa\u8d28\u91cf\u5728\u5019\u9009\u7ec4\u91cc\u6311\u9009\u4ee3\u8868\u3002\u56e0\u6b64\uff0c\u540c\u6837\u5750\u6807\u7684\u4e24\u5bf9\u8bfb\u6bb5\u6709\u53ef\u80fd\u4fdd\u7559\u5176\u4e2d\u4e00\u5bf9\uff0c\u518d\u7ed9\u53e6\u4e00\u5bf9\u6807\u4e0a\u91cd\u590d\u4f4d\u3002\u6587\u5e93\u4fe1\u606f\u4e00\u65e6\u5212\u9519\u7ec4\uff0c\u5de5\u5177\u6bd4\u8f83\u7684\u5bf9\u8c61\u96c6\u5408\u5c31\u53d1\u751f\u53d8\u5316\u3002\u5bf9\u4e8e\u9ad8\u5ea6\u5bcc\u96c6\u7684\u5c0f\u9776\u533a\u6216\u56fa\u5b9a\u6269\u589e\u5f15\u7269\uff0c\u5927\u91cf\u4e0d\u540c\u5206\u5b50\u53ef\u80fd\u5929\u7136\u5177\u6709\u76f8\u8fd1\u7684\u7aef\u70b9\uff0c\u89e3\u91ca\u4f4d\u7f6e\u91cd\u590d\u65f6\u8981\u7ed3\u5408\u5b9e\u9a8c\u8bbe\u8ba1\u3002Picard MarkDuplicates \u5b98\u65b9\u53c2\u6570\u8bf4\u660e<\/a><\/p>\n

\u5b9e\u8dd1\u7ecf\u9a8c\uff5c\u4e24\u4e2a\u8bfb\u7ec4\u662f\u5426\u5c5e\u4e8e\u540c\u4e00\u4efd\u6587\u5e93<\/h2>\n

\u5b89\u88c5 Picard 3.1.1\uff0c\u6784\u9020\u4e00\u4e2a\u6837\u672c\u3001\u4e24\u4e2a\u8bfb\u7ec4\u3001\u4e09\u5bf9\u8bfb\u6bb5\u3002\u7b2c\u4e00\u5bf9\u4e0e\u7b2c\u4e8c\u5bf9\u90fd\u4ece\u4e00\u767e\u96f6\u4e00\u548c\u4e00\u767e\u516b\u5341\u4e00\u8fd9\u4e24\u4e2a\u4f4d\u7f6e\u5f00\u59cb\uff0c\u6bd4\u5bf9\u65b9\u5411\u4e00\u81f4\uff0c\u4e24\u7aef\u5404\u957f\u4e09\u5341\u4e2a\u78b1\u57fa\u3002\u7b2c\u4e00\u5bf9\u6240\u6709\u78b1\u57fa\u7684\u8d28\u91cf\u503c\u4e3a\u56db\u5341\uff0c\u7b2c\u4e8c\u5bf9\u4e3a\u4e8c\u5341\u3002\u7b2c\u4e09\u5bf9\u7684\u8d28\u91cf\u8f83\u4f4e\uff0c\u4f46\u4f4d\u7f6e\u6362\u5230\u56db\u767e\u4e8c\u5341\u4e00\u548c\u4e94\u767e\u96f6\u4e00\uff0c\u4f5c\u4e3a\u989d\u5916\u5bf9\u7167\u3002\u6211\u4eec\u6309\u5750\u6807\u6392\u5e8f\u8f93\u5165\uff0c\u4f7f\u7528\u4e25\u683c\u683c\u5f0f\u68c0\u67e5\u548c\u9ed8\u8ba4\u7684\u6807\u8bb0\u7b56\u7565\u3002\u4eba\u5de5\u540d\u5b57\u4e0d\u542b\u6d4b\u5e8f\u4eea\u56fe\u5757\u6216\u50cf\u7d20\u5750\u6807\uff0c\u56e0\u6b64\u672c\u6b21\u5173\u95ed\u5149\u5b66\u91cd\u590d\u8bc6\u522b\uff0c\u53ea\u8003\u5bdf\u4f4d\u7f6e\u548c\u6587\u5e93\u3002<\/p>\n

\n\n\n\n\n\n\n\n\n
\u6bd4\u8f83\u9879\u76ee<\/th>\n\u4e24\u4e2a\u8bfb\u7ec4\u540c\u5c5e\u6587\u5e93 A<\/th>\n\u7b2c\u4e8c\u4e2a\u8bfb\u7ec4\u5c5e\u4e8e\u6587\u5e93 B<\/th>\n<\/tr>\n<\/thead>\n
\u8f93\u5165\uff0f\u8f93\u51fa\u7684\u6bd4\u5bf9\u8bb0\u5f55<\/td>\n6\uff0f6<\/td>\n6\uff0f6<\/td>\n<\/tr>\n
\u6587\u5e93\u5c42\u9762\u7684\u5df2\u68c0\u67e5\u8bfb\u5bf9<\/td>\nA \u4e3a 3 \u5bf9<\/td>\nA \u4e3a 1 \u5bf9\uff0cB \u4e3a 2 \u5bf9<\/td>\n<\/tr>\n
\u6807\u8bb0\u7684\u91cd\u590d\u8bfb\u5bf9<\/td>\nA \u4e3a 1 \u5bf9<\/td>\n\u4e24\u4e2a\u6587\u5e93\u5747\u4e3a 0<\/td>\n<\/tr>\n
\u88ab\u6807\u8bb0\u7684\u4e24\u6761\u8bb0\u5f55<\/td>\nlow\uff0cFLAG 1123 \u4e0e 1171<\/td>\n\u65e0<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\"\u91cd\u590d\u6807\u8bb0\u4ece\u54ea\u91cc\u6765\u3002\u4e09\u5bf9\u8bfb\u6bb5\u3001\u4e24\u4e2a\u8bfb\u7ec4\u3001\u4e00\u4e2a\u6837\u672c\uff0c\u53ea\u6539\u7b2c\u4e8c\u4e2a\u8bfb\u7ec4\u7684\u6587\u5e93\u6807\u8bc6\u3002\u540c\u4e00\u6587\u5e93\uff0c1
\u4e09\u5bf9\u8bfb\u6bb5\u3001\u4e24\u4e2a\u8bfb\u7ec4\u3001\u4e00\u4e2a\u6837\u672c\uff0c\u53ea\u6539\u7b2c\u4e8c\u4e2a\u8bfb\u7ec4\u7684\u6587\u5e93\u6807\u8bc6\u3002<\/figcaption><\/figure>\n

\u7b2c\u4e00\u6b21\u8fd0\u884c\u7684\u91cd\u590d\u5bf9\u6570\u4e3a\u4e00\uff0c\u6307\u6807\u8868\u91cc\u7684\u91cd\u590d\u6bd4\u4f8b\u4e3a\u96f6\u70b9\u4e09\u4e09\u4e09\u4e09\u4e09\u4e09\u3002\u89c2\u5bdf\u88ab\u6807\u8bb0\u7684\u5b9e\u9645\u8bb0\u5f55\uff0c\u4e24\u6761\u90fd\u53eb low\uff0c\u5bf9\u5e94\u90a3\u5bf9\u8d28\u91cf\u8f83\u4f4e\u3001\u5750\u6807\u76f8\u540c\u7684\u8bfb\u6bb5\u3002\u5b83\u4eec\u539f\u5148\u7684\u6807\u5fd7\u5206\u522b\u662f\u4e5d\u5341\u4e5d\u548c\u4e00\u767e\u56db\u5341\u4e03\uff0c\u52a0\u4e0a\u6570\u503c\u4e3a\u4e00\u5343\u96f6\u4e8c\u5341\u56db\u7684\u91cd\u590d\u4f4d\u540e\uff0c\u53d8\u6210\u4e00\u5343\u4e00\u767e\u4e8c\u5341\u4e09\u548c\u4e00\u5343\u4e00\u767e\u4e03\u5341\u4e00\u3002\u6309\u91cd\u590d\u6807\u5fd7\u7b5b\u9009\u4f1a\u5f97\u5230\u4e24\u884c\uff0c\u6307\u6807\u8868\u5219\u6309\u8bfb\u5bf9\u8bb0\u4e00\uff0c\u4e24\u8005\u53ef\u4ee5\u9010\u884c\u5bf9\u4e0a\u3002\u7b2c\u4e09\u5bf9\u5c3d\u7ba1\u8d28\u91cf\u4e5f\u8f83\u4f4e\uff0c\u56e0\u4e3a\u7aef\u70b9\u4e0d\u540c\uff0c\u4e24\u6b21\u90fd\u4fdd\u7559\u4e0b\u6765\u3002<\/p>\n

\u7b2c\u4e8c\u6b21\u4ec5\u6539\u53d8\u7b2c\u4e8c\u4e2a\u8bfb\u7ec4\u5728\u6587\u4ef6\u5934\u4e2d\u7684\u6587\u5e93\u540d\u79f0\u3002\u7b2c\u4e00\u6b21\u548c\u7b2c\u4e8c\u6b21\u6d4b\u91cf\u5b9e\u9645\u90fd\u8f93\u51fa\u516d\u884c\uff0c\u533a\u522b\u662f\u7b2c\u4e8c\u6b21\u516d\u884c\u91cc\u6ca1\u6709\u4efb\u4f55\u4e00\u884c\u5e26\u91cd\u590d\u6807\u5fd7\u3002\u68c0\u67e5\u6307\u6807\u8868\u8fd8\u4f1a\u770b\u5230\u539f\u6765\u5355\u72ec\u7684\u4e00\u884c\u62c6\u6210\u4e24\u884c\uff0c\u5206\u522b\u68c0\u67e5\u4e00\u5bf9\u548c\u4e24\u5bf9\u3002\u8de8\u6587\u5e93\u6c47\u603b\u65f6\u5e94\u7d2f\u52a0\u5206\u6bcd\u548c\u5206\u5b50\uff0c\u518d\u8ba1\u7b97\u5b9e\u9a8c\u8981\u7528\u7684\u6574\u4f53\u6bd4\u4f8b\uff0c\u7279\u522b\u662f\u4e00\u4e2a\u6587\u5e93\u6bd4\u53e6\u4e00\u4e2a\u6df1\u5f88\u591a\u65f6\uff0c\u76f4\u63a5\u5e73\u5747\u4e24\u4e2a\u6587\u5e93\u7684\u767e\u5206\u6bd4\u4f1a\u6539\u53d8\u6bcf\u5bf9\u8bfb\u6bb5\u7684\u6743\u91cd\u3002<\/p>\n

samtools view -H shared.bam | awk '$1=="@RG"'\r\njava -Xmx512m -jar picard.jar MarkDuplicates I=shared.bam O=marked.bam M=metrics.txt READ_NAME_REGEX=null\r\nsamtools view -f 0x400 marked.bam | cut -f1,2\r\nsamtools view -c -F 0x400 marked.bam\r\n<\/code><\/pre>\n
\u5bf9\u672c\u4f8b\u505a\u4e00\u9879\u7b80\u4fbf\u7684\u53cd\u7b97\uff0c\u7b2c\u4e00\u6b21\u516d\u6761\u8f93\u51fa\u8bb0\u5f55\u4e2d\u6709\u4e24\u6761\u5e26\u91cd\u590d\u4f4d\uff0c\u4f59\u4e0b\u56db\u6761\uff0c\u6b63\u597d\u5bf9\u5e94\u4e24\u5bf9\u3002\u7b2c\u4e8c\u6b21\u6392\u9664\u91cd\u590d\u4f4d\u540e\u4ecd\u6709\u516d\u6761\u3002\u6b63\u5f0f\u6570\u636e\u5e38\u540c\u65f6\u542b\u6709\u672a\u914d\u5bf9\u3001\u672a\u6bd4\u5bf9\u3001\u6b21\u8981\u6216\u8865\u5145\u8bb0\u5f55\uff0c\u6307\u6807\u8868\u7ed9\u8fd9\u4e9b\u8bb0\u5f55\u5355\u8bbe\u4e86\u5b57\u6bb5\uff0c\u4e0d\u80fd\u628a\u4efb\u610f\u4e24\u4e2a\u547d\u4ee4\u5f97\u5230\u7684\u884c\u6570\u90fd\u76f4\u63a5\u9664\u4ee5\u4e8c\u3002<\/p>\n
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