{"id":636,"date":"2013-03-12T09:47:37","date_gmt":"2013-03-12T01:47:37","guid":{"rendered":"http:\/\/www.hzaumycology.com\/chenlianfu_blog\/?p=636"},"modified":"2013-06-12T16:41:53","modified_gmt":"2013-06-12T08:41:53","slug":"samtools%e4%bb%8b%e7%bb%8d","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=636","title":{"rendered":"SAM\u683c\u5f0f\u7b80\u4ecb"},"content":{"rendered":"

\u67e5\u770b\u6587\u732e\u8bf7\u70b9\u51fb\uff1aThe Sequence Alignment\/Map format and SAMtools<\/a>\u3002\u4e5f\u53ef\u4ee5google\u641c\u7d22\u201cThe SAM Format Specification\u201d\u67e5\u8be2SAM Format\u7684\u8be6\u7ec6\u6587\u6863\u3002
\nSAMtools\u4f5c\u4e3a\u4e00\u4e2a\u901a\u7528\u5de5\u5177\uff0c\u4f7f\u7528\u5404\u79cd\u65b9\u6cd5\u6765\uff0c\u4ee5SAM\u683c\u5f0f\u6765\u5bf9reads\u7684\u6bd4\u5bf9\u7ed3\u679c\u8fdb\u884c\u9884\u5904\u7406\u3002\u6bd4\u5982\uff1a\u7d22\u5f15\u6392\u5e8f\uff0c\u67e5\u627e\u53d8\u5f02\u548c\u6bd4\u5bf9\u67e5\u770b\u7b49\u3002
\nSAM\u683c\u5f0f\u7531\u4e24\u90e8\u5206\u7ec4\u6210\uff1a\u5934\u90e8\u533a\u548c\u6bd4\u5bf9\u533a\uff0c\u90fd\u4ee5tab\u5206\u5217\u3002<\/p>\n

\u5934\u90e8\u533a:\u4ee5\u2018@\u2019\u5f00\u59cb\uff0c\u4f53\u73b0\u4e86\u6bd4\u5bf9\u7684\u4e00\u4e9b\u603b\u4f53\u4fe1\u606f\u3002\u6bd4\u5bf9\u7684SAM\u683c\u5f0f\u7248\u672c\uff0c\u6bd4\u5bf9\u7684\u53c2\u8003\u5e8f\u5217\uff0c\r\n\u6bd4\u5bf9\u4f7f\u7528\u7684\u8f6f\u4ef6\u7b49\u3002\r\n\u6bd4\u5bf9\u533a: \u6bd4\u5bf9\u7ed3\u679c\uff0c\u6bcf\u4e00\u4e2a\u6bd4\u5bf9\u7ed3\u679c\u662f\u4e00\u884c\uff0c\u670911\u4e2a\u4e3b\u5217\u548c1\u4e2a\u53ef\u9009\u5217\u3002<\/pre>\n
@HD VN:1.0 SO:unsorted <\/span> \r\n\u5934\u90e8\u533a\u7b2c\u4e00\u884c\uff1aVN\u662f\u683c\u5f0f\u7248\u672c\uff1bSO\u8868\u793a\u6bd4\u5bf9\u6392\u5e8f\u7684\u7c7b\u578b\uff0c\u6709unkown(default),unsorted,\r\nqueryname\u548ccoordinate\u51e0\u79cd\u3002samtools\u8f6f\u4ef6\u5728\u8fdb\u884c\u6392\u5e8f\u540e\u4e0d\u80fd\u81ea\u52a8\u66f4\u65b0bam\u6587\u4ef6\u7684SO\u503c\u3002\r\npicard\u5374\u53ef\u4ee5\u3002\r\n@SQ SN:A.auricula_all_contig_1 LN:9401<\/span>\r\n\u53c2\u8003\u5e8f\u5217\u540d\u3002\u8fd9\u4e9b\u53c2\u8003\u5e8f\u5217\u51b3\u5b9a\u4e86\u6bd4\u5bf9\u7ed3\u679csort\u7684\u987a\u5e8f\u3002SN\u662f\u53c2\u8003\u5e8f\u5217\u540d\uff1bLN\u662f\u53c2\u8003\u5e8f\u5217\r\n\u957f\u5ea6;\r\n@RG ID:sample01<\/span>\r\nRead Group. 1\u4e2asample\u7684\u6d4b\u5e8f\u7ed3\u679c\u4e3a1\u4e2aRead Group\uff1b\u8be5sample\u53ef\u4ee5\u6709\u591a\u4e2alibrary\r\n\u7684\u6d4b\u5e8f\u7ed3\u679c\u3002\r\n@PG ID:bowtie2 PN:bowtie2 VN:2.0.0-beta7<\/span>\r\n\u6bd4\u5bf9\u6240\u4f7f\u7528\u7684\u8f6f\u4ef6\u3002<\/pre>\n
\u6bd4\u5bf9\u533a11\u4e2a\u5217\u548c\u53ef\u9009\u5217\u7684\u89e3\u91ca<\/span>\r\n1  QNAME  \u6bd4\u5bf9\u7684\u5e8f\u5217\u540d\r\n2  FLAG   Bwise FLAG(\u8868\u660e\u6bd4\u5bf9\u7c7b\u578b\uff1apairing\uff0cstrand\uff0cmate strand\u7b49)\r\n3  RNAME  \u6bd4\u5bf9\u4e0a\u7684\u53c2\u8003\u5e8f\u5217\u540d\r\n4  POS    1-Based\u7684\u6bd4\u5bf9\u4e0a\u7684\u6700\u5de6\u8fb9\u7684\u5b9a\u4f4d\r\n5  MAPQ   \u6bd4\u5bf9\u8d28\u91cf\r\n6  CIGAR  Extended CIGAR string (\u64cd\u4f5c\u7b26\uff1aMIDNSHP) \u6bd4\u5bf9\u7ed3\u679c\u4fe1\u606f\uff1a\u5339\u914d\u78b1\u57fa\u6570\uff0c\u53ef\u53d8\u526a\u63a5\u7b49\u3002\r\n7  MRNM   \u76f8\u5339\u914d\u7684\u53e6\u5916\u4e00\u6761\u5e8f\u5217\uff0c\u6bd4\u5bf9\u4e0a\u7684\u53c2\u8003\u5e8f\u5217\u540d\r\n8  MPOS   1-Based leftmost Mate POsition\r\n9  ISIZE  \u63d2\u5165\u7247\u6bb5\u957f\u5ea6\r\n10 SEQ    \u548c\u53c2\u8003\u5e8f\u5217\u5728\u540c\u4e00\u4e2a\u740f\u4e0a\u7684\u6bd4\u5bf9\u5e8f\u5217(\u82e5\u6bd4\u5bf9\u7ed3\u679c\u5728\u8d1f\u610f\u94fe\u4e0a\uff0c\u5219\u5e8f\u5217\u662f\u5176\u53cd\u5411\u91cd\u590d\u5e8f\u5217)\r\n11 QUAL   \u6bd4\u5bf9\u5e8f\u5217\u7684\u8d28\u91cf(ASCII-33=Phred base quality)\r\n12 \u53ef\u9009\u7684\u884c\uff0c\u4ee5TAG\uff1aTYPE\uff1aVALUE\u7684\u5f62\u5f0f\u63d0\u4f9b\u989d\u5916\u7684\u4fe1\u606f<\/pre>\n
\u6bd4\u5bf9\u533a\u7b2c2\u5217FLAG\u8bf4\u660e\uff1a\r\nBitwise\uff08\u6309\u4f4d\u8ba1\u7b97\uff09\r\nBit(0x\u8868\u793a\u5341\u516d\u8fdb\u5236) \u5341\u8fdb\u5236\u6570\u503c Description\r\n0x1    1   \u6bd4\u5bf9\u65f6\u6709\u591a\u4e2a\u79cd\u5b50\u5e8f\u5217\u6bd4\u5bf9\u4e0a<\/pre>\n","protected":false},"excerpt":{"rendered":"
\u67e5\u770b\u6587\u732e\u8bf7\u70b9\u51fb\uff1aThe Sequence Alignment\/Map forma … \u7ee7\u7eed\u9605\u8bfb →<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[3],"tags":[31],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/636"}],"collection":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=636"}],"version-history":[{"count":18,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/636\/revisions"}],"predecessor-version":[{"id":1503,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/636\/revisions\/1503"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=636"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=636"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=636"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}