{"id":2103,"date":"2014-06-09T14:20:23","date_gmt":"2014-06-09T06:20:23","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2103"},"modified":"2014-06-09T14:49:23","modified_gmt":"2014-06-09T06:49:23","slug":"bwa%e7%9a%84%e4%bd%bf%e7%94%a8","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2103","title":{"rendered":"bwa\u7684\u4f7f\u7528"},"content":{"rendered":"<h1>1. \u7b80\u4ecb<\/h1>\n<p>\u6700\u8fd1\u9700\u8981\u4f7f\u7528\u8f6f\u4ef6GAM-NGS\u8f6f\u4ef6\uff0c\u4f46\u662f\u8be5\u8f6f\u4ef6\u8c8c\u4f3c\u4e0d\u652f\u6301bowtie2\u7684\u7ed3\u679c\u3002\u53ef\u80fd\u9700\u8981\u7528\u5230BWA\uff0c\u4e8e\u662f\u53c2\u8003<a href=\"http:\/\/bio-bwa.sourceforge.net\/\" target=\"_blank\">BWA\u7684\u7f51\u7ad9<\/a>\u53ca<a href=\"http:\/\/bio-bwa.sourceforge.net\/bwa.shtml\" target=\"_blank\">\u5176Manual<\/a>\u3002<br \/>\nbwa\uff0c\u5373Burrows-Wheeler-Alignment Tool\u3002<br \/>\nBWA \u5305\u542b 3 \u79cd\u7b97\u6cd5\uff1a<\/p>\n<pre>\r\nBWA-bactrack: \u7528\u4e8e\u8fdb\u884c Illumina reads \u7684\u6bd4\u5bf9\u3002reads \u7684\u957f\u5ea6\u6700\u5927\u4e3a 100bp\u3002\r\nBWA-SW: \u7528\u4e8e\u6bd4\u5bf9 long-read \uff0c\u652f\u6301\u7684\u957f\u5ea6\u4e3a 70bp-1Mbp\uff1b\u540c\u65f6\u652f\u6301\u526a\u63a5\u6027\u6bd4\u5bf9\u3002\r\nBWA-MEM: \u6700\u65b0\u7684\u7b97\u6cd5\u3002\u548c BWA-SW \u7684\u9002\u7528\u6027\u4e00\u81f4\uff0c\u4f46\u662f\u66f4\u52a0\u5feb\u901f\u548c\u51c6\u786e\uff1b\u540c\u65f6\u4e0e BWA-bactrack \u76f8\u6bd4\uff0c\u5728\u5bf9 70-100bp reads \u7684\u6bd4\u5bf9\u4e0a\u6709\u66f4\u4f18\u7684\u6027\u80fd\u3002\r\n<\/pre>\n<h1>2. BWA \u7684\u4e0b\u8f7d\u548c\u5b89\u88c5<\/h1>\n<pre>\r\n$ wget http:\/\/jaist.dl.sourceforge.net\/project\/bio-bwa\/bwa-0.7.9a.tar.bz2\r\n$ tar jxf bwa-0.7.9a.tar.bz2 -C \/opt\/biosoft\/\r\n$ cd \/opt\/biosoft\/bwa-0.7.9a\/\r\n$ make\r\n$ echo 'PATH=$PATH:\/opt\/biosoft\/bwa-0.7.9a' >> ~\/.bashrc\r\n$ source ~\/.bashrc\r\n<\/pre>\n<h1>3. BWA\u7528\u6cd5<\/h1>\n<h2>2.1 index<\/h2>\n<p>\u5728\u8fdb\u884c reads \u7684\u6bd4\u5bf9\u524d\uff0c\u9700\u8981\u5bf9 fasta \u6587\u4ef6\u6784\u5efa FM-index\u3002<br \/>\n\u5e38\u7528\u4f8b\u5b50\u548c\u53c2\u6570\u5982\u4e0b\uff1a<\/p>\n<pre>\r\n$ bwa index ref.fa -p genome\r\n\r\n-p STR\r\n\u8f93\u51fa\u7684\u6570\u636e\u5e93\u524d\u7f00\u3002 \u9ed8\u8ba4\u548c\u8f93\u5165\u7684\u6587\u4ef6\u540d\u4e00\u81f4\uff0c\u5219\u8f93\u51fa\u7684\u6570\u636e\u5e93\u5728\u5176\u8f93\u5165\u6587\u4ef6\u6240\u5728\u7684\u6587\u4ef6\u5939\uff0c\u5e76\u4ee5\u8be5\u6587\u4ef6\u540d\u4e3a\u524d\u7f00\u3002\r\n-a [is|bwtsw]\r\n\u8f93\u5165\u6784\u5efa index \u7684\u7b97\u6cd5\u3002 is \u7b97\u6cd5\u7b80\u5355\u5feb\u901f\uff0c\u662f\u9ed8\u8ba4\u7684\u9009\u9879\uff0c\u4f46\u662f\u4e0d\u80fd\u7528\u4e8e\u57fa\u56e0\u7ec4\u5927\u4e8e 2GB \u7684\u6570\u636e\u5e93\uff1b bwtsw \u9002\u5408\u4e8e\u5927\u57fa\u56e0\u7ec4\uff0c\u6bd4\u5982\u4eba\u7c7b\u57fa\u56e0\u7ec4\u3002\r\n<\/pre>\n<h2>2.2 mem<\/h2>\n<p>\u8be5\u7b97\u6cd5\u5148\u4f7f\u7528 MEM(maximal exact matches) \u8fdb\u884c seeding alignments\uff0c\u518d\u4f7f\u7528 SW(affine-gap Smith-Waterman) \u7b97\u6cd5\u8fdb\u884c seeds \u7684\u5ef6\u4f38\u3002<br \/>\nBWA&#8211;MEM \u7b97\u6cd5\u6267\u884c\u5c40\u90e8\u6bd4\u5bf9\u548c\u526a\u63a5\u6027\u3002\u53ef\u80fd\u4f1a\u51fa\u73b0 query \u5e8f\u5217\u7684\u591a\u4e2a\u4e0d\u540c\u7684\u90e8\u4f4d\u51fa\u73b0\u5404\u81ea\u7684\u6700\u4f18\u5339\u914d\uff0c\u5bfc\u81f4 reads \u6709\u591a\u4e2a\u6700\u4f73\u5339\u914d\u4f4d\u70b9\u3002\u8fd9\u5bf9 long reads \u7684\u6bd4\u5bf9\u65f6\u6bd4\u8f83\u91cd\u8981\u7684\u7ed3\u679c\u3002\u4f46\u662f\u5374\u4f1a\u548c Picard \u7684 markDuplicates \u7a0b\u5e8f\u90e8\u517c\u5bb9\u3002<br \/>\n\u5e38\u7528\u4f8b\u5b50\u548c\u53c2\u6570\u5982\u4e0b\uff1a<\/p>\n<pre>\r\n$ bwa mem genome reads.fq > aln-se.sam\r\n$ bwa mem genome read1.fq read2.fq > aln-pe.sam\r\n\r\n-t INT\r\n\u4f7f\u7528\u7684\u7ebf\u7a0b\u6570\r\n-p\r\n\u82e5\u65e0\u6b64\u53c2\u6570\uff1a\u8f93\u5165\u6587\u4ef6\u53ea\u67091\u4e2a\uff0c\u5219\u8fdb\u884c\u5355\u7aef\u6bd4\u5bf9\uff1b\u82e5\u8f93\u5165\u6587\u4ef6\u67092\u4e2a\uff0c\u5219\u4f5c\u4e3apaired reads\u8fdb\u884c\u6bd4\u5bf9\u3002\u82e5\u52a0\u5165\u6b64\u53c2\u6570\uff1a\u5219\u4ec5\u4ee5\u7b2c1\u4e2a\u6587\u4ef6\u4f5c\u4e3a\u8f93\u5165(\u8f93\u5165\u7684\u6587\u4ef6\u82e5\u67092\u4e2a\uff0c\u5219\u5ffd\u7565\u4e4b)\uff0c\u8be5\u6587\u4ef6\u5fc5\u987b\u662fread1.fq\u548cread2.fa\u8fdb\u884creads\u4ea4\u53c9\u7684\u6570\u636e\u3002\r\n-M\r\n\u52a0\u5165\u6b64\u53c2\u6570\u7528\u4e8e\u5c06 shorter split hits \u6807\u8bb0\u4e3a\u6b21\u4f18\uff0c\u6709\u5229\u4e8e\u517c\u5bb9 Picard\u3002\r\n<\/pre>\n<h2>2.3 bwasw<\/h2>\n<p>\u5bf9\u8f93\u5165\u7684\u7b2c1\u4e2a\u6587\u4ef6\u7684\u6240\u6709\u5e8f\u5217\u8fdb\u884c\u6bd4\u5bf9\u3002\u5982\u679c\u8f93\u5982\u6709 2 \u4e2a\u6587\u4ef6\uff0c\u5219\u8fdb\u884c paired-end \u6bd4\u5bf9\uff0c\u6b64\u6a21\u5f0f\u4ec5\u5bf9 Illumina \u7684 short-insert \u6570\u636e\u8fdb\u884c\u6bd4\u5bf9\u3002\u5728 Paired-end \u6a21\u5f0f\u4e0b\uff0cBWA-SW\u4f9d\u7136\u8f93\u51fa\u526a\u63a5\u6027\u6bd4\u5bf9\u7ed3\u679c\uff0c\u4f46\u662f\u8fd9\u4e9b\u7ed3\u679c\u4f1a\u6807\u8bb0\u4e3a not properly paired; \u540c\u65f6\u5982\u679c\u6709\u591a\u4e2a\u5339\u914d\u4f4d\u70b9\uff0c\u5219\u4e0d\u4f1a\u5199\u5165 mate \u7684\u5339\u914d\u4f4d\u7f6e\u3002<br \/>\n\u5e38\u7528\u4f8b\u5b50\u548c\u53c2\u6570\u5982\u4e0b\uff1a<\/p>\n<pre>\r\n$ bwa bwasw genome long_read.fq > aln.sam\r\n$ bwa bwasw genome read1.fq read2.fq > aln-pe.sam\r\n\r\n-t INT\r\n\u4f7f\u7528\u7684\u7ebf\u7a0b\u6570\r\n<\/pre>\n<h2>2.4 backtrack<\/h2>\n<p>\u7ecf\u5178\u7684 bwa \u5148\u4f7f\u7528 aln \u547d\u4ee4\u5c06\u5355\u72ec\u7684 reads \u6bd4\u5bf9\u5230\u53c2\u8003\u5e8f\u5217\uff0c\u518d\u4f7f\u7528 samse \u6216 sampe \u751f\u6210 sam \u6587\u4ef6\u3002<br \/>\n\u5e38\u7528\u4f8b\u5b50\uff1a<\/p>\n<pre>\r\n$ bwa aln genome read1.fq > aln_sa1.sai\r\n$ bwa aln genome read2.fq > aln_sa2.sai\r\n$ bwa samse genome aln_sa1.sai read1.fq > aln_se.sam\r\n$ bwa sampe genome aln_sa1.sai aln_sa2.sai read1.fq read2.fq > aln_pe.sam\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>1. \u7b80\u4ecb \u6700\u8fd1\u9700\u8981\u4f7f\u7528\u8f6f\u4ef6GAM-NGS\u8f6f\u4ef6\uff0c\u4f46\u662f\u8be5\u8f6f\u4ef6\u8c8c\u4f3c\u4e0d\u652f\u6301bowtie &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=2103\">\u7ee7\u7eed\u9605\u8bfb <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[1],"tags":[],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2103"}],"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=2103"}],"version-history":[{"count":3,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2103\/revisions"}],"predecessor-version":[{"id":2106,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2103\/revisions\/2106"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2103"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2103"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2103"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}