{"id":2309,"date":"2015-08-25T16:48:31","date_gmt":"2015-08-25T08:48:31","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2309"},"modified":"2015-08-25T16:48:31","modified_gmt":"2015-08-25T08:48:31","slug":"samtools-%e5%92%8c-bamtools-%e5%ae%89%e8%a3%85","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2309","title":{"rendered":"samtools \u548c bamtools \u5b89\u88c5"},"content":{"rendered":"<h1>1. samtools \u5b89\u88c5<\/h1>\n<p>SAMtools \u65b0\u7684 1.0 \u7248\u672c\u6539\u8fdb\u6bd4\u8f83\u5927\u3002 SAMtools \u5305\u542b 3 \u90e8\u5206\uff1a<\/p>\n<pre>\r\nSamtools : \u5bf9 SAM\/BAM\/CRAM \u683c\u5f0f\u6587\u4ef6\u8fdb\u884c\u8bfb\u3001\u5199\u3001\u7d22\u5f15\u548c\u67e5\u770b\u64cd\u4f5c\u3002\r\nBCFtools : \u5bf9 BCF2\/VCF\/gVCF \u683c\u5f0f\u6587\u4ef6\u8fdb\u884c\u8bfb\u5199\u64cd\u4f5c\uff1b \u5bf9 SNP \u548c short indel \u8fdb\u884c calling\/filtering\/summarising\r\nHTSlib : \u7528\u4e8e\u9ad8\u901a\u91cf\u6570\u636e\u8bfb\u5199\u64cd\u4f5c\u7684 C library\r\n<\/pre>\n<p>\u65b0\u7248\u7684 samtools \u5c06 Samtools \u548c BCFtool \u5206\u79bb\u5f00\uff0c\u6210\u4e3a 2 \u4e2a\u72ec\u7acb\u7684\u8f6f\u4ef6\u5305\u3002 \u8fd9 2 \u4e2a\u90fd\u8fd0\u7528\u4e86 HTSlib\uff0c\u5e76\u4e14\u5176\u8f6f\u4ef6\u5305\u4e2d\u90fd\u5305\u542b\u4e86 HTSlib \u3002<br \/>\n\u65b0\u7248\u4e0d\u7684 Samtools \u7684\u5b98\u65b9\u7f51\u5740\u66f4\u6539\u4e3a\u4e86\uff1a <a href=\"http:\/\/www.htslib.org\/\" target=\"_blank\">http:\/\/www.htslib.org\/<\/a><\/p>\n<h2>1.1 \u5b89\u88c5 Samtools<\/h2>\n<pre>\r\n$ wget http:\/\/downloads.sourceforge.net\/project\/samtools\/samtools\/1.1\/samtools-1.1.tar.bz2\r\n$ tar jxf samtools-1.1.tar.bz2 -C \/opt\/biosoft\/\r\n$ cd \/opt\/biosoft\/samtools-1.1\/\r\n$ make -j 8\r\n$ echo 'PATH=$PATH:\/opt\/biosoft\/samtools-1.1\/' >> ~\/.bashrc\r\n<\/pre>\n<h2>1.2 \u5b89\u88c5 BCFtools<\/h2>\n<pre>\r\n$ wget http:\/\/sourceforge.net\/projects\/samtools\/files\/samtools\/1.1\/bcftools-1.1.tar.bz2\r\n$ tar jxf bcftools-1.1.tar.bz2 -C \/opt\/biosoft\/\r\n$ cd \/opt\/biosoft\/bcftools-1.1\r\n$ make -j 8\r\n$ echo 'PATH=$PATH:\/opt\/biosoft\/bcftools-1.1' >> ~\/.bashrc\r\n<\/pre>\n<h1>2. Bamtools<\/h1>\n<p>Bamtools \u662f Samtools \u7684 c++ \u7248\u672c\u7684 Samtools\uff0c \u5176\u5b98\u7f51\uff1a <a href=\"https:\/\/github.com\/pezmaster31\/bamtools\" target=\"_blank\">https:\/\/github.com\/pezmaster31\/bamtools<\/a><\/p>\n<pre>\r\n$ wget https:\/\/github.com\/pezmaster31\/bamtools\/archive\/master.zip -O bamtools-master.zip\r\n$ unzip bamtools-master.zip -d \/opt\/biosoft\/\r\n$ cd \/opt\/biosoft\/bamtools-master\/\r\n$ mkdir build\r\n$ cd build\/\r\n$ cmake ..\r\n$ make -j 8\r\n$ echo 'PATH=$PATH:\/opt\/biosoft\/bamtools-master\/bin\/' >> ~\/.bashrc \r\n$ source ~\/.bashrc\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>1. samtools \u5b89\u88c5 SAMtools \u65b0\u7684 1.0 \u7248\u672c\u6539\u8fdb\u6bd4\u8f83\u5927\u3002  &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=2309\">\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":[3],"tags":[70],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2309"}],"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=2309"}],"version-history":[{"count":1,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2309\/revisions"}],"predecessor-version":[{"id":2310,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2309\/revisions\/2310"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2309"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2309"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2309"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}