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wrap;\">\u76ee\u524d\uff0c\u6709\u8bb8\u591a\u5de5\u5177\u53ef\u4ee5\u7528\u6765\u6ce8\u91ca\u53d8\u5f02\uff0c\u4f46\u5176\u4e2d\u4e00\u4e2a\u6bd4\u8f83\u6d41\u884c\u548c\u5f3a\u5927\u7684\u662fsnpEFF\u3002snpEFF\u662f\u4e00\u4e2a\u5f00\u6e90\u7684Java\u7a0b\u5e8f\uff0c\u53ef\u4ee5\u5bf9VCF\u683c\u5f0f\u7684\u53d8\u5f02\u6587\u4ef6\u8fdb\u884c\u5feb\u901f\u548c\u51c6\u786e\u7684\u6ce8\u91ca\u3002snpEFF\u53ef\u4ee5\u9884\u6d4b\u53d8\u5f02\u5bf9\u8f6c\u5f55\u672c\u548c\u86cb\u767d\u8d28\u7684\u5f71\u54cd\uff0c\u4f8b\u5982\u9519\u4e49\u3001\u65e0\u4e49\u3001\u526a\u5207\u4f4d\u70b9\u3001\u542f\u52a8\u5b50\u3001\u7ec8\u6b62\u5b50\u7b49\u3002snpEFF\u8fd8\u53ef\u4ee5\u63d0\u4f9b\u5176\u4ed6\u6709\u7528\u7684\u4fe1\u606f\uff0c\u4f8b\u5982\u57fa\u56e0\u540d\u3001\u8f6c\u5f55\u672cID\u3001\u5916\u663e\u5b50\u7f16\u53f7\u3001\u5bc6\u7801\u5b50\u6539\u53d8\u3001\u6c28\u57fa\u9178\u6539\u53d8\u7b49\uff1bsnpEFF\u652f\u6301\u5305\u62ec\u4eba\u7c7b\u3001\u52a8\u7269\u3001\u690d\u7269\u3001\u5fae\u751f\u7269\u7b49\u8d85\u8fc738,000\u4e2a\u7269\u79cd\u7684\u57fa\u56e0\u7ec4\u6570\u636e\u5e93\uff0c\u4e5f\u53ef\u4ee5\u81ea\u5b9a\u4e49\u6570\u636e\u5e93\u6216\u4f7f\u7528\u516c\u5171\u6570\u636e\u5e93\u3002\u652f\u6301\u591a\u79cd\u53d8\u5f02\u683c\u5f0f\uff0c\u5305\u62ecVCF\u3001GFF\u3001BED\u7b49\uff1b\u652f\u6301\u591a\u79cd\u8f93\u51fa\u683c\u5f0f\uff0c\u5305\u62ec\u6587\u672c\u3001HTML\u3001VCF\u7b49\uff1b\u652f\u6301\u591a\u79cd\u7edf\u8ba1\u5206\u6790\uff0c\u5305\u62ec\u53d8\u5f02\u9891\u7387\u3001\u53d8\u5f02\u7c7b\u578b\u5206\u5e03\u3001\u53d8\u5f02\u529f\u80fd\u5206\u5e03\u7b49\u3002<\/p>\n<p style=\"text-indent: 0em;text-wrap: wrap;\">snpEFF\u7684\u4f7f\u7528\u975e\u5e38\u7b80\u5355\uff0c\u53ea\u9700\u8981\u51e0\u4e2a\u547d\u4ee4\u884c\u53c2\u6570\u5c31\u53ef\u4ee5\u8fd0\u884c\u3002snpEFF\u7684\u4f7f\u7528\u5305\u62ec\u4ee5\u4e0b\u51e0\u6b65\uff0c\u9996\u5148\u9700\u8981\u4e0b\u8f7dsnpEFF\u548c\u76f8\u5e94\u7684\u57fa\u56e0\u7ec4\u6570\u636e\u5e93\u6216\u8005\u81ea\u5b9a\u4e49\u6570\u636e\u5e93\u3002\u7136\u540e\u4f7f\u7528snpEff\u547d\u4ee4\u5bf9VCF\u6587\u4ef6\u8fdb\u884c\u6ce8\u91ca\uff0c\u6307\u5b9a\u6570\u636e\u5e93\u540d\u79f0\u548c\u8f93\u51fa\u6587\u4ef6\u540d\u3002\u6700\u540e\uff0c\u53ef\u4ee5\u4f7f\u7528snpEff\u7684\u4f34\u968f\u5de5\u5177SnpSift\u5bf9\u6ce8\u91ca\u7ed3\u679c\u8fdb\u884c\u8fc7\u6ee4\u3001\u6392\u5e8f\u6216\u7edf\u8ba1\u3002snpEFF\u8fd8\u53ef\u4ee5\u4e0e\u5176\u4ed6\u5de5\u5177\u96c6\u6210\uff0c\u4f8b\u5982GATK\u3001bcftools\u6216VEP\u3002<\/p>\n<\/section>\n<section style=\"text-align: left;justify-content: flex-start;margin: 20px 0%;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;min-width: 10%;flex: 0 0 auto;height: auto;background-color: rgb(204, 223, 237);border-width: 0px;border-radius: 0px 50px 50px 0px;border-style: none;border-color: rgb(62, 62, 62);padding-right: 10px;align-self: flex-start;\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;min-width: 10%;flex: 0 0 auto;height: auto;background-color: rgb(60, 86, 125);border-width: 0px;border-radius: 0px 50px 50px 0px;border-style: none;border-color: rgb(62, 62, 62);align-self: flex-start;\">\n<section style=\"color: rgb(255, 255, 254);line-height: 2;padding-right: 15px;padding-left: 15px;text-align: justify;\" powered-by=\"xiumi.us\">\n<p><strong>1. snpEFF\u7684\u4e0b\u8f7d\u4e0e\u5b89\u88c5<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p style=\"text-indent: 0em;text-wrap: wrap;\"><strong>\u65b9\u6cd5\u4e00\uff0c\u4e0b\u8f7d\u538b\u7f29\u5305\u5b89\u88c5\u3002<\/strong><span style=\"text-indent: 0em;\">\u4e0b\u8f7d\u7f51\u5740\uff1ahttps:\/\/sourceforge.net\/projects\/snpeff\/ <\/span><\/p>\n<p style=\"text-indent: 0em;text-wrap: wrap;\">\u4e0b\u8f7d\u89e3\u538b\u540e\uff0c\u4f1a\u5728snpEff\u6587\u4ef6\u5939\u4e2d\u751f\u4ea7\u4e24\u4e2ajar\u5305snpEff.jar\u548cSnpSift.jar\u3002\u8fd0\u884c\u547d\u4ee4java -jar snpEff.jar \u751f\u6210\u5e2e\u52a9\u6587\u4ef6\u5219\u5b89\u88c5\u6210\u529f\u3002<\/p>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.6351851851851852\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_YeARiaXhD3ic9bta9FtDTmNqXpFBIw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSNSNSA4ZJsgLwqzl7vCHyYhMGc3NHWNaIJ9zQmVr0iaAEoqhUYeARiaXhD3ic9bta9FtDTmNqXpFBIw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p><strong>\u65b9\u6cd5\u4e8c\uff0c\u4f7f\u7528conda\u5b89\u88c5snpEFF\u3002<\/strong><\/p>\n<p>conda\u662f\u53ef\u4ee5\u65b9\u4fbf\u5730\u5b89\u88c5\u548c\u66f4\u65b0\u5404\u79cd\u8f6f\u4ef6\u3002\u8981\u4f7f\u7528conda\u5b89\u88c5snpEFF\uff0c\u9996\u5148\u9700\u8981\u5b89\u88c5conda\uff0c\u53ef\u4ee5\u53c2\u8003\u5b98\u65b9\u7f51\u7ad9\u7684\u6559\u7a0b\uff1ahttps:\/\/docs.conda.io\/en\/latest\/miniconda.html \u3002\u5b89\u88c5\u597dconda\u540e\uff0c\u6253\u5f00\u7ec8\u7aef\uff0c\u8f93\u5165\u4ee5\u4e0b\u547d\u4ee4\uff1a<\/p>\n<p>conda install -c bioconda snpeff<\/p>\n<p>\u8fd9\u4e2a\u547d\u4ee4\u4f1a\u4ecebioconda\u9891\u9053\u4e0b\u8f7d\u5e76\u5b89\u88c5snpEFF\u53ca\u5176\u4f9d\u8d56\u7684\u8f6f\u4ef6\u5305\u3002\u5b89\u88c5\u5b8c\u6210\u540e\uff0c\u53ef\u4ee5\u4f7f\u7528\u4ee5\u4e0b\u547d\u4ee4\u68c0\u67e5snpEFF\u7684\u7248\u672c\uff1a<\/p>\n<p>snpeff -version<\/p>\n<p>\u5982\u679c\u663e\u793aSnpEff\u7248\u672c\u4fe1\u606f\uff0c\u8bf4\u660esnpEFF\u5df2\u7ecf\u6210\u529f\u5b89\u88c5\u3002<\/p>\n<\/section>\n<section style=\"text-align: left;justify-content: flex-start;margin: 20px 0%;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;min-width: 10%;flex: 0 0 auto;height: auto;background-color: rgb(204, 223, 237);border-width: 0px;border-radius: 0px 50px 50px 0px;border-style: none;border-color: rgb(62, 62, 62);padding-right: 10px;align-self: flex-start;\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;min-width: 10%;flex: 0 0 auto;height: auto;background-color: rgb(60, 86, 125);border-width: 0px;border-radius: 0px 50px 50px 0px;border-style: none;border-color: rgb(62, 62, 62);align-self: flex-start;\">\n<section style=\"color: rgb(255, 255, 254);line-height: 2;padding-right: 15px;padding-left: 15px;text-align: justify;\" powered-by=\"xiumi.us\">\n<p><strong>2. \u4e0b\u8f7d\u6216\u6784\u5efa\u6570\u636e\u5e93<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-indent: 0em;text-wrap: wrap;\"><strong>\u65b9\u6cd5\u4e00\uff1a\u4f7f\u7528snpEFF\u81ea\u5e26\u7684\u6570\u636e\u5e93<\/strong><\/p>\n<p style=\"text-indent: 0em;text-wrap: wrap;\">snpEFF\u81ea\u5e26\u4e86\u4e00\u4e9b\u5e38\u89c1\u7269\u79cd\u7684\u6570\u636e\u5e93\uff0c\u5982\u4eba\u7c7b\u3001\u5c0f\u9f20\u3001\u5927\u80a0\u6746\u83cc\u7b49\uff0c\u8fd9\u4e9b\u6570\u636e\u5e93\u53ef\u4ee5\u76f4\u63a5\u4e0b\u8f7d\u4f7f\u7528\u3002\u4e0b\u8f7d\u7684\u547d\u4ee4\u5982\u4e0b\uff1a<\/p>\n<p style=\"text-indent: 0em;text-wrap: wrap;\">java -jar snpEff.jar download -v hg19<\/p>\n<p style=\"text-indent: 0em;text-wrap: wrap;\">\u5176\u4e2dhg19\u662f\u4eba\u7c7b\u57fa\u56e0\u7ec4\u7684\u7248\u672c\u53f7\uff0c\u53ef\u4ee5\u6839\u636e\u9700\u8981\u66ff\u6362\u4e3a\u5176\u4ed6\u7269\u79cd\u548c\u7248\u672c\u3002\u4e0b\u8f7d\u5b8c\u6210\u540e\uff0c\u53ef\u4ee5\u5728snpEff\/data\u76ee\u5f55\u4e0b\u770b\u5230\u76f8\u5e94\u7684\u6587\u4ef6\u5939\uff0c\u91cc\u9762\u5305\u542b\u4e86\u57fa\u56e0\u7ec4\u5e8f\u5217\u548c\u6ce8\u91ca\u4fe1\u606f\u3002<\/p>\n<p style=\"text-indent: 0em;text-wrap: wrap;\"><strong>\u65b9\u6cd5\u4e8c\uff1a\u4f7f\u7528GFF3\u6216GTF\u6587\u4ef6\u5efa\u5e93<\/strong><\/p>\n<p style=\"text-indent: 0em;text-wrap: wrap;\">\u5982\u679csnpEFF\u6ca1\u6709\u63d0\u4f9b\u6240\u9700\u7269\u79cd\u7684\u6570\u636e\u5e93\uff0c\u6216\u8005\u9700\u8981\u4f7f\u7528\u81ea\u5df1\u7684\u6ce8\u91ca\u4fe1\u606f\uff0c\u53ef\u4ee5\u4f7f\u7528GFF3\u6216GTF\u6587\u4ef6\u6765\u5efa\u5e93\u3002\u8fd9\u4e9b\u6587\u4ef6\u53ef\u4ee5\u4ece\u5404\u79cd\u6570\u636e\u5e93\u6216\u7f51\u7ad9\u4e0b\u8f7d\uff0c\u4e5f\u53ef\u4ee5\u81ea\u5df1\u751f\u6210\u3002\u4f7f\u7528GFF3\u6216GTF\u6587\u4ef6\u5efa\u5e93\u7684\u547d\u4ee4\u5982\u4e0b\uff1a<\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">java -jar snpEff.jar build -<span class=\"code-snippet__built_in\">c<\/span> snpEff.config -gff3 -v my_genome<\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-indent: 0em;text-wrap: wrap;\" powered-by=\"xiumi.us\">\u5176\u4e2dmy_genome\u662f\u81ea\u5b9a\u4e49\u7684\u6570\u636e\u5e93\u540d\u79f0\uff0c\u53ef\u4ee5\u968f\u610f\u6307\u5b9a\u3002-c\u6307\u5b9a\u914d\u7f6e\u6587\u4ef6snpEff.config\uff0c-v\u6307\u5b9a\u5197\u957f\u6a21\u5f0f\u3002-gff3\u8868\u793a\u4f7f\u7528GFF3\u683c\u5f0f\u7684\u6587\u4ef6\uff0c\u5982\u679c\u662fGTF\u683c\u5f0f\uff0c\u5219\u6539\u4e3a-gtf\u3002\u5728\u6267\u884c\u547d\u4ee4\u4e4b\u524d\uff0c\u9700\u8981\u5148\u5728snpEff\/data\u76ee\u5f55\u4e0b\u521b\u5efa\u4e00\u4e2a\u4ee5my_genome\u4e3a\u540d\u7684\u6587\u4ef6\u5939\uff0c\u5e76\u5c06\u57fa\u56e0\u7ec4\u5e8f\u5217\u548cGFF3\u6216GTF\u6587\u4ef6\u653e\u5165\u5176\u4e2d\u3002\u57fa\u56e0\u7ec4\u5e8f\u5217\u5fc5\u987b\u547d\u540d\u4e3amy_genome.fa\uff0cGFF3\u6216GTF\u6587\u4ef6\u5fc5\u987b\u547d\u540d\u4e3agenes.gff\u6216genes.gtf\u3002\u5e76\u5728snpEff.config\u914d\u7f6e\u6587\u4ef6\u6700\u540e\u4e00\u884c\u52a0\u5165\uff1amy_genome.genome : my_genome\u3002<\/p>\n<section style=\"text-align: left;justify-content: flex-start;margin: 20px 0%;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;min-width: 10%;flex: 0 0 auto;height: auto;background-color: rgb(204, 223, 237);border-width: 0px;border-radius: 0px 50px 50px 0px;border-style: none;border-color: rgb(62, 62, 62);padding-right: 10px;align-self: flex-start;\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;min-width: 10%;flex: 0 0 auto;height: auto;background-color: rgb(60, 86, 125);border-width: 0px;border-radius: 0px 50px 50px 0px;border-style: none;border-color: rgb(62, 62, 62);align-self: flex-start;\">\n<section style=\"color: rgb(255, 255, 254);line-height: 2;padding-right: 15px;padding-left: 15px;text-align: justify;\" powered-by=\"xiumi.us\">\n<p><strong>3. snpEFF\u7684\u4f7f\u7528\u65b9\u6cd5<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p><strong>snpEFF\u7684\u57fa\u672c\u7528\u6cd5\u662f\uff1a<\/strong><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">java -jar snpEff.jar [options] genome_version input_file > output_file\u5176\u4e2d\uff1a- genome_version\uff1a<\/span><\/code><\/pre>\n<\/section>\n<section style=\"padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p>\u6307\u5b9a\u8981\u4f7f\u7528\u7684\u53c2\u8003\u57fa\u56e0\u7ec4\u548c\u6ce8\u91ca\u6570\u636e\u5e93\u7684\u7248\u672c\uff0c\u5982GRCh38.99\u3001hg19\u7b49\u3002\u53ef\u4ee5\u4f7f\u7528`java -jar snpEff.jar databases`\u547d\u4ee4\u67e5\u770b\u53ef\u7528\u7684\u6570\u636e\u5e93\u5217\u8868\u3002- input_file\uff1a\u6307\u5b9a\u8981\u6ce8\u91ca\u7684\u53d8\u5f02\u6587\u4ef6\uff0c\u53ef\u4ee5\u662fVCF\u3001GFF\u3001BED\u7b49\u683c\u5f0f\uff0c\u4e5f\u53ef\u4ee5\u662f\u6807\u51c6\u8f93\u5165\uff08stdin\uff09\u3002- output_file\uff1a\u6307\u5b9a\u8f93\u51fa\u6587\u4ef6\uff0c\u53ef\u4ee5\u662f\u6807\u51c6\u8f93\u51fa\uff08stdout\uff09\uff0c\u4e5f\u53ef\u4ee5\u662f\u4e00\u4e2a\u6587\u4ef6\u540d\u3002\u8f93\u51fa\u6587\u4ef6\u9ed8\u8ba4\u662fVCF\u683c\u5f0f\uff0c\u4e5f\u53ef\u4ee5\u901a\u8fc7\u53c2\u6570\u6307\u5b9a\u5176\u4ed6\u683c\u5f0f\u3002snpEFF\u7684\u5e38\u89c1\u53c2\u6570\u548c\u9009\u9879snpEFF\u6709\u5f88\u591a\u53c2\u6570\u548c\u9009\u9879\uff0c\u53ef\u4ee5\u6839\u636e\u9700\u8981\u8fdb\u884c\u8c03\u6574\u3002\u4ee5\u4e0b\u662f\u4e00\u4e9b\u5e38\u89c1\u7684\u53c2\u6570\u548c\u9009\u9879\uff1a- -v\uff1a\u663e\u793a\u8be6\u7ec6\u4fe1\u606f\uff0c\u5305\u62ec\u7a0b\u5e8f\u7248\u672c\u3001\u6570\u636e\u5e93\u7248\u672c\u3001\u8fd0\u884c\u65f6\u95f4\u7b49\u3002- -noLog\uff1a\u4e0d\u8f93\u51fa\u65e5\u5fd7\u4fe1\u606f\u3002- -noStats\uff1a\u4e0d\u8f93\u51fa\u7edf\u8ba1\u4fe1\u606f\u3002- -no-downstream\uff1a\u4e0d\u6ce8\u91ca\u4e0b\u6e38\u533a\u57df\uff08\u9ed8\u8ba4\u4e3a5kb\uff09\u7684\u53d8\u5f02\u3002- -no-upstream\uff1a\u4e0d\u6ce8\u91ca\u4e0a\u6e38\u533a\u57df\uff08\u9ed8\u8ba4\u4e3a5kb\uff09\u7684\u53d8\u5f02\u3002- -no-intergenic\uff1a\u4e0d\u6ce8\u91ca\u95f4\u57fa\u56e0\u533a\u57df\u7684\u53d8\u5f02\u3002- -no-intron\uff1a\u4e0d\u6ce8\u91ca\u5185\u542b\u5b50\u533a\u57df\u7684\u53d8\u5f02\u3002- -no-utr\uff1a\u4e0d\u6ce8\u91caUTR\u533a\u57df\u7684\u53d8\u5f02\u3002- -formatEff\uff1a\u8f93\u51fa\u683c\u5f0f\u4e3aEFF\u683c\u5f0f\uff0c\u800c\u4e0d\u662fVCF\u683c\u5f0f\u3002EFF\u683c\u5f0f\u662f\u4e00\u79cd\u7b80\u5316\u7684\u683c\u5f0f\uff0c\u53ea\u5305\u542b\u53d8\u5f02\u7684\u5f71\u54cd\u548c\u4e25\u91cd\u7a0b\u5ea6\u7b49\u4fe1\u606f\u3002- -csvStats\uff1a\u8f93\u51fa\u7edf\u8ba1\u4fe1\u606f\u4e3aCSV\u683c\u5f0f\uff0c\u800c\u4e0d\u662fHTML\u683c\u5f0f\u3002CSV\u683c\u5f0f\u65b9\u4fbf\u7528\u5176\u4ed6\u8f6f\u4ef6\u8fdb\u884c\u5206\u6790\u548c\u7ed8\u56fe\u3002<\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">\u793a\u4f8b\u547d\u4ee4\uff1a<\/span><\/code><code><span class=\"code-snippet_outer\">java -Xmx4G -jar snpEff.jar eff -csvStats variants.SnpEff.csv -s variants.SnpEff.html -<span class=\"code-snippet__built_in\">c<\/span> snpEff.config -v -ud <span class=\"code-snippet__number\">500<\/span> my_genome my_snp.vcf > my.SnpEff.vcf<\/span><\/code><\/pre>\n<\/section>\n<ul class=\"list-paddingleft-1\" style=\"padding-left: 40px;list-style-position: outside;\" powered-by=\"xiumi.us\">\n<li>\n<p>-Xmx2G\u6307\u5b9aJava\u865a\u62df\u673a\u7684\u6700\u5927\u5806\u5927\u5c0f\u4e3a4GB\u3002<\/p>\n<\/li>\n<li>\n<p>-csvStats variants.SnpEff.csv \u6307\u5b9a\u8f93\u51faCSV\u683c\u5f0f\u7684\u7edf\u8ba1\u4fe1\u606f\u3002<\/p>\n<\/li>\n<li>\n<p>-s variants.SnpEff.html \u6307\u5b9a\u8f93\u51faHTML\u683c\u5f0f\u7684\u6458\u8981\u62a5\u544a\u3002<\/p>\n<\/li>\n<li>\n<p>-ud 500\u6307\u5b9a\u4e0a\u6e38\/\u4e0b\u6e38\u533a\u95f4\u957f\u5ea6\u4e3a500\u4e2a\u78b1\u57fa\u3002<\/p>\n<\/li>\n<li>\n<p>my_genome \u6307\u5b9a\u8981\u4f7f\u7528\u7684\u57fa\u56e0\u7ec4\u3002<\/p>\n<\/li>\n<li>\n<p>my_snp.vcf \u6307\u5b9a\u8f93\u5165VCF\u6587\u4ef6\u3002<\/p>\n<\/li>\n<\/ul>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">\u7ed3\u675f\u540e\u5171\u8f93\u51fa<span class=\"code-snippet__number\">4<\/span>\u4e2a\u6587\u4ef6\uff1avariants.SnpEff.csv\u3001variants.SnpEff.html\u3001my.SnpEff.vcf\u3001my.SnpEff.genes.txt\u3002<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: left;justify-content: flex-start;margin: 20px 0%;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;min-width: 10%;flex: 0 0 auto;height: auto;background-color: rgb(204, 223, 237);border-width: 0px;border-radius: 0px 50px 50px 0px;border-style: none;border-color: rgb(62, 62, 62);padding-right: 10px;align-self: flex-start;\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;min-width: 10%;flex: 0 0 auto;height: auto;background-color: rgb(60, 86, 125);border-width: 0px;border-radius: 0px 50px 50px 0px;border-style: none;border-color: rgb(62, 62, 62);align-self: flex-start;\">\n<section style=\"color: rgb(255, 255, 254);line-height: 2;padding-right: 15px;padding-left: 15px;text-align: justify;\" powered-by=\"xiumi.us\">\n<p><strong>4. snpEFF\u6ce8\u91ca\u7ed3\u679c\u89e3\u8bfb<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p>HTML\u683c\u5f0f\u7684\u6458\u8981\u62a5\u544a\u662f\u4e00\u4e2a\u7f51\u9875\u6587\u4ef6\uff0c\u53ef\u4ee5\u7528\u6d4f\u89c8\u5668\u6253\u5f00\u3002\u5b83\u5305\u542b\u4e86\u4ee5\u4e0b\u51e0\u4e2a\u90e8\u5206\uff1a<\/p>\n<\/section>\n<ul style=\"list-style-type: \uf0b7;padding-left: 40px;list-style-position: outside;\" class=\"list-paddingleft-1\" powered-by=\"xiumi.us\">\n<li>\n<p>Summary\uff1a\u8fd9\u90e8\u5206\u663e\u793a\u4e86\u4e00\u4e9b\u57fa\u672c\u7684\u4fe1\u606f\uff0c\u5982\u57fa\u56e0\u7ec4\u540d\u79f0\u3001\u6ce8\u91ca\u65e5\u671f\u3001\u6ce8\u91ca\u547d\u4ee4\u3001\u8b66\u544a\u4fe1\u606f\u3001\u9519\u8bef\u4fe1\u606f\u3001\u8f93\u5165\u6587\u4ef6\u884c\u6570\u3001\u53d8\u5f02\u4f4d\u70b9\u6570\uff08\u8fc7\u6ee4\u524d\u540e\uff09\u3001\u975e\u53d8\u5f02\u4f4d\u70b9\u6570\u3001\u5177\u6709ID\u7684\u53d8\u5f02\u4f4d\u70b9\u6570\u3001\u975e\u53cc\u7b49\u4f4d\u57fa\u56e0\u7ec4SNP\u4f4d\u70b9\u6570\u3001Number of effects\u3001\u53c2\u8003\u57fa\u56e0\u7ec4\u603b\u957f\u5ea6\u3001\u53c2\u8003\u57fa\u56e0\u7ec4\u6709\u6548\u957f\u5ea6\u3001\u53d8\u5f02\u7387\u7b49\u3002<\/p>\n<\/li>\n<\/ul>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.4462962962962963\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-09-20_\u300c\u8f6c\u300dSnpEff\uff1a\u4e00\u4e2a\u795e\u5947\u7684\u57fa\u56e0\u7ec4\u53d8\u5f02\u6ce8\u91ca\u5de5\u5177\/2_oicMr4Oe0BM8FKG37nIdniafnIv63Q.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSNSNSA4ZJsgLwqzl7vCHyYPp4UIRiaUiadnoG34xt9WNTCMKh6oicMr4Oe0BM8FKG37nIdniafnIv63Q\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section style=\"padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<ul style=\"list-style-type: \uf0b7;padding-left: 40px;list-style-position: outside;\" class=\"list-paddingleft-1\">\n<li>\n<p>Variant types\uff1a\u8fd9\u90e8\u5206\u663e\u793a\u4e86\u4e0d\u540c\u7c7b\u578b\u7684\u53d8\u5f02\u7684\u6570\u91cf\u548c\u767e\u5206\u6bd4\uff0c\u5305\u62ecSNP\uff08\u5355\u6838\u82f7\u9178\u591a\u6001\u6027\uff09\u3001MNP\uff08\u591a\u6838\u82f7\u9178\u591a\u6001\u6027\uff09\u3001INS\uff08\u63d2\u5165\u53d8\u5f02\uff09\u3001DEL\uff08\u7f3a\u5931\u53d8\u5f02\uff09\u3001MIXED\uff08\u6df7\u5408\u53d8\u5f02\uff09\u3001INV (\u5012\u4f4d\u53d8\u5f02\uff09\u3001DUP\uff08\u91cd\u590d\u53d8\u5f02\uff09\u3001BED\uff08\u6613\u4f4d\u53d8\u5f02\uff09\u3001INTERVAL\uff08\u95f4\u9694\u53d8\u5f02\uff09\u7b49\u3002<\/p>\n<\/li>\n<\/ul>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.3285198555956679\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-09-20_\u300c\u8f6c\u300dSnpEff\uff1a\u4e00\u4e2a\u795e\u5947\u7684\u57fa\u56e0\u7ec4\u53d8\u5f02\u6ce8\u91ca\u5de5\u5177\/3_eIOmnyMjO6pfTvmAkHUqpxCnq7HeYw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSNSNSA4ZJsgLwqzl7vCHyYFXW3iboUmR2tvT6hf4qh9qoLxeIOmnyMjO6pfTvmAkHUqpxCnq7HeYw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"277\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section style=\"padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<ul style=\"list-style-type: \uf0b7;padding-left: 40px;list-style-position: outside;\" class=\"list-paddingleft-1\">\n<li>\n<p>Effects by type\uff1a\u8fd9\u90e8\u5206\u663e\u793a\u4e86\u4e0d\u540c\u7c7b\u578b\u7684\u6548\u5e94\u7684\u6570\u91cf\u548c\u767e\u5206\u6bd4\uff0c\u5305\u62ec3\u2019\u7aef\u4e3b\u8981UTR\u53d8\u5f02\u30015\u2019\u7aef\u4e3b\u8981UTR\u63d0\u524d\u542f\u52a8\u5b50\u83b7\u5f97\u53d8\u5f02\u30015\u2019\u7aef\u4e3b\u8981UTR\u53d8\u5f02\u3001\u4e0b\u6e38\u57fa\u56e0\u53d8\u5f02\u3001\u8d77\u59cb\u5bc6\u7801\u5b50\u7f16\u7801\u53d8\u5f02\u3001\u57fa\u56e0\u95f4\u9694\u533a\u3001\u5185\u542b\u5b50\u53d8\u5f02\u3001\u526a\u63a5\u53d7\u4f53\u53d8\u5f02\u3001\u526a\u63a5\u4f9b\u4f53\u53d8\u5f02\u3001\u526a\u63a5\u533a\u57df\u53d8\u5f02\u3001\u8d77\u59cb\u7f3a\u5931\u3001\u8d77\u59cb\u4fdd\u7559\u53d8\u5f02\u3001\u7ec8\u6b62\u83b7\u5f97\u3001\u7ec8\u6b62\u7f3a\u5931\u3001\u7ec8\u6b62\u4fdd\u7559\u53d8\u5f02\u3001\u540c\u4e49\u53d8\u5f02\u3001\u4e0a\u6e38\u57fa\u56e0\u53d8\u5f02\u7b49\u3002<\/p>\n<\/li>\n<li>\n<p>Effects by region\uff1a\u8fd9\u90e8\u5206\u663e\u793a\u4e86\u4e0d\u540c\u533a\u57df\u7684\u6548\u5e94\u7684\u6570\u91cf\u548c\u767e\u5206\u6bd4\uff0c\u5305\u62ec\u4e0b\u6e38\u3001\u5916\u663e\u5b50\u3001\u95f4\u9694\u533a\u3001\u5185\u542b\u5b50\u3001\u526a\u63a5\u4f4d\u70b9\u53d7\u4f53\u3001\u526a\u63a5\u4f4d\u70b9\u4f9b\u4f53\u3001\u526a\u63a5\u4f4d\u70b9\u533a\u57df\u3001\u4e0a\u6e38\u30013\u2019UTR\u533a\u30015\u2019UTR\u533a\u7b49\u3002<\/p>\n<\/li>\n<\/ul>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.5972222222222222\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_W8Ey8VWJgqXicbBIFxlw0kWluf4Y6g.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSNSNSA4ZJsgLwqzl7vCHyYeC93eHiaeLmFV2Yb0bbKSHewACW8Ey8VWJgqXicbBIFxlw0kWluf4Y6g\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.3805970149253731\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-09-20_\u300c\u8f6c\u300dSnpEff\uff1a\u4e00\u4e2a\u795e\u5947\u7684\u57fa\u56e0\u7ec4\u53d8\u5f02\u6ce8\u91ca\u5de5\u5177\/5_BA8u0fT99L1pReECmzicwy1jrKfbvQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSNSNSA4ZJsgLwqzl7vCHyYfzxt1mMpEqsFu6IS6URRxPxS1BA8u0fT99L1pReECmzicwy1jrKfbvQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"938\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<ul style=\"list-style-type: \uf0b7;padding-left: 40px;list-style-position: outside;\" class=\"list-paddingleft-1\" powered-by=\"xiumi.us\">\n<li>\n<p>Effects by functional class\uff1a\u8fd9\u90e8\u5206\u663e\u793a\u4e86\u4e0d\u540c\u529f\u80fd\u7c7b\u522b\u7684\u6548\u5e94\u7684\u6570\u91cf\u548c\u767e\u5206\u6bd4\uff0c\u5305\u62ec\u65e0\u6548\u679c\uff08NONE\uff09\u3001\u4fee\u9970\u6027\uff08MODIFIER\uff09\u3001\u4f4e\u5f71\u54cd\uff08LOW\uff09\u3001\u4e2d\u7b49\u5f71\u54cd\uff08MODERATE\uff09\u3001\u9ad8\u5f71\u54cd\uff08HIGH\uff09\u7b49\u3002<\/p>\n<\/li>\n<\/ul>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.38571428571428573\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-09-20_\u300c\u8f6c\u300dSnpEff\uff1a\u4e00\u4e2a\u795e\u5947\u7684\u57fa\u56e0\u7ec4\u53d8\u5f02\u6ce8\u91ca\u5de5\u5177\/6_vgCibGLhia3sr6F5p2c0KGJ2mom1mQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSNSNSA4ZJsgLwqzl7vCHyYn4ItGJ1SwZtuZw7j4pYibq4b69ZvgCibGLhia3sr6F5p2c0KGJ2mom1mQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"420\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<ul style=\"list-style-type: \uf0b7;padding-left: 40px;list-style-position: outside;\" class=\"list-paddingleft-1\" powered-by=\"xiumi.us\">\n<li>\n<p>Transitions \/ Transversions\uff1a\u8fd9\u90e8\u5206\u663e\u793a\u4e86\u8f6c\u6362\/\u98a0\u6362\u7684\u6bd4\u4f8b\u548c\u6570\u91cf\uff0c\u4ee5\u53ca\u4e0d\u540c\u7c7b\u578b\u7684\u8f6c\u6362\/\u98a0\u6362\u7684\u6570\u91cf\u548c\u767e\u5206\u6bd4\u3002\u8f6c\u6362\u662f\u6307\u560c\u5464\u4e0e\u560c\u5464\u6216\u5627\u5576\u4e0e\u5627\u5576\u4e4b\u95f4\u7684\u66ff\u4ee3\uff0c\u98a0\u6362\u662f\u6307\u560c\u5464\u4e0e\u5627\u5576\u4e4b\u95f4\u7684\u66ff\u4ee3\u3002<\/p>\n<\/li>\n<\/ul>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.39299610894941633\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_piaxOvoEKtW2icgicGCmuRsB8MqvtA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSNSNSA4ZJsgLwqzl7vCHyYyngmsTyWgwVNvXUXfWGRwBEh8ZJpiaxOvoEKtW2icgicGCmuRsB8MqvtA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"257\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<ul style=\"list-style-type: \uf0b7;padding-left: 40px;list-style-position: outside;\" class=\"list-paddingleft-1\" powered-by=\"xiumi.us\">\n<li>\n<p>Allele frequency histogram\uff1a\u8fd9\u90e8\u5206\u663e\u793a\u4e86\u7b49\u4f4d\u57fa\u56e0\u9891\u7387\u7684\u76f4\u65b9\u56fe\uff0c\u6a2a\u5750\u6807\u4e3a\u7b49\u4f4d\u57fa\u56e0\u9891\u7387\uff0c\u7eb5\u5750\u6807\u4e3a\u6570\u91cf\u3002<\/p>\n<\/li>\n<li>\n<p>Allele count histogram\uff1a\u8fd9\u90e8\u5206\u663e\u793a\u4e86\u7b49\u4f4d\u57fa\u56e0\u6570\u91cf\u7684\u76f4\u65b9\u56fe\uff0c\u6a2a\u5750\u6807\u4e3a\u7b49\u4f4d\u57fa\u56e0\u6570\u91cf\uff0c\u7eb5\u5750\u6807\u4e3a\u6570\u91cf\u3002<\/p>\n<\/li>\n<li>\n<p>Genotype summary\uff1a\u8fd9\u90e8\u5206\u663e\u793a\u4e86\u6837\u672c\u57fa\u56e0\u578b\u7684\u6c47\u603b\u4fe1\u606f\uff0c\u5305\u62ec\u6742\u5408\u57fa\u56e0\u578b\uff08HETEROZYGOUS\uff09\u3001\u7eaf\u5408\u57fa\u56e0\u578b\uff08HOMOZYGOUS\uff09\u3001\u7f3a\u5931\u57fa\u56e0\u578b\uff08MISSING\uff09\u7b49\u3002<\/p>\n<\/li>\n<li>\n<p>Codon change histogram\uff1a\u8fd9\u90e8\u5206\u663e\u793a\u4e86\u5bc6\u7801\u5b50\u6539\u53d8\u7684\u76f4\u65b9\u56fe\uff0c\u6a2a\u5750\u6807\u4e3a\u5bc6\u7801\u5b50\u6539\u53d8\u7c7b\u578b\uff0c\u7eb5\u5750\u6807\u4e3a\u6570\u91cf\u3002\u5bc6\u7801\u5b50\u6539\u53d8\u662f\u6307\u5355\u6838\u82f7\u9178\u7a81\u53d8\u5bfc\u81f4\u5bc6\u7801\u5b50\u53d1\u751f\u6539\u53d8\u3002<\/p>\n<\/li>\n<li>\n<p>Amino acid change histogram\uff1a\u8fd9\u90e8\u5206\u663e\u793a\u4e86\u6c28\u57fa\u9178\u6539\u53d8\u7684\u76f4\u65b9\u56fe\uff0c\u6a2a\u5750\u6807\u4e3a\u6c28\u57fa\u9178\u6539\u53d8\u7c7b\u578b\uff0c\u7eb5\u5750\u6807\u4e3a\u6570\u91cf\u3002\u6c28\u57fa\u9178\u6539\u53d8\u662f\u6307\u5355\u6838\u82f7\u9178\u7a81\u53d8\u5bfc\u81f4\u5bc6\u7801\u5b50\u53d1\u751f\u6539\u53d8\uff0c\u8fdb\u800c\u5bfc\u81f4\u6c28\u57fa\u9178\u53d1\u751f\u6539\u53d8\uff08\u9519\u4e49\u7a81\u53d8\uff09\u3002<\/p>\n<\/li>\n<li>\n<p>Chromosome summary\uff1a\u8fd9\u90e8\u5206\u663e\u793a\u4e86\u67d3\u8272\u4f53\u7684\u6c47\u603b\u4fe1\u606f\uff0c\u5305\u62ec\u67d3\u8272\u4f53\u540d\u79f0\u3001\u53c2\u8003\u57fa\u56e0\u7ec4\u957f\u5ea6\u3001\u6709\u6548\u957f\u5ea6\u3001\u53d8\u5f02\u4f4d\u70b9\u6570\u3001\u53d8\u5f02\u7387\u7b49\u3002<\/p>\n<\/li>\n<\/ul>\n<p style=\"text-indent: 0em;text-wrap: wrap;\" powered-by=\"xiumi.us\">snpEFF\u662f\u4e00\u4e2a\u975e\u5e38\u5f3a\u5927\u800c\u53c8\u65b9\u4fbf\u7684\u6ce8\u91ca\u5de5\u5177\uff0c\u6211\u5f3a\u70c8\u63a8\u8350\u5927\u5bb6\u5c1d\u8bd5\u4e00\u4e0b\u3002\u5982\u679c\u4f60\u60f3\u4e86\u89e3\u66f4\u591a\u5173\u4e8esnpEFF\u7684\u4fe1\u606f\uff0c\u4f60\u53ef\u4ee5\u8bbf\u95ee\u5b83\u7684\u5b98\u7f51\uff1ahttp:\/\/snpeff.sourceforge.net\/\u3002\u5982\u679c\u4f60\u6709\u4efb\u4f55\u5173\u4e8esnpEFF\u7684\u95ee\u9898\u6216\u5efa\u8bae\uff0c\u4f60\u53ef\u4ee5\u5728\u8bc4\u8bba\u533a\u7559\u8a00\uff0c\u6211\u4f1a\u5c3d\u5feb\u56de\u590d\u4f60\u3002\u8c22\u8c22\u5927\u5bb6\u7684\u9605\u8bfb\uff0c\u4e0b\u6b21\u518d\u89c1\uff01<\/p>\n<section style=\"margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"box-shadow: rgb(170, 170, 170) 0px 0px 10px inset;border-color: rgb(192, 200, 209);padding: 10px;border-width: 1px;border-style: solid;background-color: rgb(250, 250, 239);\">\n<section style=\"color: rgb(51, 51, 51);text-align: center;padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p style=\"text-align: justify;text-wrap: wrap;\">\u5927\u6d77\u54e5\u4eca\u5929\u7684\u8bb2\u89e3\u5c31\u5230\u8fd9\u91cc\u4e86~\u4e0b\u671f\u6211\u5c06\u4f1a\u5e26\u6765\u5bf9\u5355\u7ec6\u80de\u6d4b\u5e8f\u5206\u6790\u7ed3\u679c\u7684\u89e3\u8bfb~\u6211\u4eec\u4e0d\u89c1\u4e0d\u6563<\/p>\n<p style=\"text-align: justify;text-wrap: wrap;\">\uff08\u6700\u540e\u63a8\u8350\u4e00\u4e0b\u5927\u6d77\u54e5\u65b0\u5f00\u53d1\u7684\u96f6\u4ee3\u7801\u4e91\u751f\u4fe1\u5206\u6790\u5de5\u5177\u5e73\u53f0\u5305\u542b\u8d85\u591a\u96f6\u4ee3\u7801\u5c0f\u5de5\u5177\uff0c\u4e0a\u4f20\u6570\u636e\u4e00\u952e\u51fa\u56fe\uff0c\u611f\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u6b22\u8fce\u6765\u53c2\u89c2\u54df\u3002<\/p>\n<p style=\"text-align: justify;text-wrap: wrap;\">\u7f51\u5740\uff1a<\/p>\n<p style=\"text-align: justify;text-wrap: wrap;\">http:\/\/www.biocloudservice.com\/home.html\uff09<\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"text-align: center;justify-content: center;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: auto;align-self: center;flex: 0 0 auto;min-width: 5%;height: auto;\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;margin-left: -6px;\">\n<section style=\"transform: rotateZ(45deg);\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;\">\n<section style=\"display: inline-block;width: 16px;height: 16px;vertical-align: top;overflow: hidden;border-style: solid;border-width: 3px 3px 0px 0px;border-color: rgb(231, 215, 173) rgb(231, 215, 173) rgb(69, 107, 176) rgb(69, 107, 176);\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;margin-left: -6px;\">\n<section style=\"transform: rotateZ(45deg);\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;\">\n<section style=\"display: inline-block;width: 16px;height: 16px;vertical-align: top;overflow: hidden;border-style: solid;border-width: 3px 3px 0px 0px;border-color: rgb(231, 215, 173) rgb(231, 215, 173) rgb(69, 107, 176) rgb(69, 107, 176);\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;margin-left: -6px;\">\n<section style=\"transform: rotateZ(45deg);\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;\">\n<section style=\"display: inline-block;width: 16px;height: 16px;vertical-align: top;overflow: hidden;border-style: solid;border-width: 3px 3px 0px 0px;border-color: rgb(231, 215, 173) rgb(231, 215, 173) rgb(69, 107, 176) rgb(69, 107, 176);\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: 38%;align-self: center;flex: 0 0 auto;height: auto;padding: 3px 23px;\">\n<section style=\"line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.025925925925926\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-09-20_\u300c\u8f6c\u300dSnpEff\uff1a\u4e00\u4e2a\u795e\u5947\u7684\u57fa\u56e0\u7ec4\u53d8\u5f02\u6ce8\u91ca\u5de5\u5177\/8_TWJ3kzibpSGVa8eGU12mTqKM8Gaxlg.jpg\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/YHGRXkSxjSSNSNSA4ZJsgLwqzl7vCHyYQSicvJKOZmicqPQLGWgNibtHtSlFTWJ3kzibpSGVa8eGU12mTqKM8Gaxlg\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: auto;align-self: center;flex: 0 0 auto;min-width: 5%;height: auto;\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;transform: rotateY(180deg);\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;margin-left: -6px;\">\n<section style=\"transform: rotateZ(45deg);\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;\">\n<section style=\"display: inline-block;width: 16px;height: 16px;vertical-align: top;overflow: hidden;border-style: solid;border-width: 3px 3px 0px 0px;border-color: rgb(231, 215, 173) rgb(231, 215, 173) rgb(69, 107, 176) rgb(69, 107, 176);\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;margin-left: -6px;\">\n<section style=\"transform: rotateZ(45deg);\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;\">\n<section style=\"display: inline-block;width: 16px;height: 16px;vertical-align: top;overflow: hidden;border-style: solid;border-width: 3px 3px 0px 0px;border-color: rgb(231, 215, 173) rgb(231, 215, 173) rgb(69, 107, 176) rgb(69, 107, 176);\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;margin-left: -6px;\">\n<section style=\"transform: rotateZ(45deg);\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;\">\n<section style=\"display: inline-block;width: 16px;height: 16px;vertical-align: top;overflow: hidden;border-style: solid;border-width: 3px 3px 0px 0px;border-color: rgb(231, 215, 173) rgb(231, 215, 173) rgb(69, 107, 176) rgb(69, 107, 176);\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"text-align: center;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"color: rgb(231, 215, 173);\">\n<p><strong>\u751f\u4fe1\u6ee9\u516c\u4f17\u53f7<\/strong><\/p>\n<\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><a target=\"_blank\" href=\"https:\/\/mp.weixin.qq.com\/s?__biz=MzAwNjE0MDY3MQ==&mid=2650761303&idx=2&sn=6f73471d1e82c56c0b2160d0fcd32d53&scene=21#wechat_redirect\" textvalue=\"\" linktype=\"image\" imgurl=\"https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/YHGRXkSxjSSYqN0u6bwwXzLCBdlX9BXOYJyjlsib6bQ74Wibtria9gSC4sqocafb5YBQcZWdQRrtP2Xo7vaFWaecA\/0?wx_fmt=jpeg\" imgdata=\"[object Object]\" tab=\"innerlink\" data-linktype=\"1\" rel=\"noopener\"><span class=\"js_jump_icon h5_image_link\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.35083798882681566\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/9_ocafb5YBQcZWdQRrtP2Xo7vaFWaecA-2.jpg?w=640\" 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powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 0px;height: 0px;vertical-align: top;overflow: hidden;border-style: solid;border-width: 0px 0px 4px 4px;border-color: rgba(255, 255, 255, 0) rgba(255, 255, 255, 0) rgba(255, 255, 255, 0) rgb(59, 149, 115);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p style=\"text-indent: 0em;text-wrap: wrap;\">\u5728\u751f\u7269\u4fe1\u606f\u5b66\u4e2d\uff0c\u5206\u6790\u57fa\u56e0\u7ec4\u53d8\u5f02\u662f\u4e00\u4e2a\u91cd\u8981\u7684\u4efb\u52a1\u3002\u53d8\u5f02\u53ef\u4ee5\u662f\u5355\u6838\u82f7\u9178\u591a\u6001\u6027\uff08SNP\uff09\u3001\u63d2\u5165\u7f3a\u5931\uff08indel\uff09\u6216\u7ed3\u6784\u53d8\u5f02\uff08SV\uff09\u3002\u53d8\u5f02\u7684\u7c7b\u578b\u548c\u5f71\u54cd\u4e0d\u540c\uff0c\u53ef\u80fd\u5bfc\u81f4\u57fa\u56e0\u8868\u8fbe\u3001\u86cb\u767d\u8d28\u529f\u80fd\u6216\u8868\u578b\u7684\u6539\u53d8\u3002\u56e0\u6b64\uff0c\u5bf9\u53d8\u5f02\u8fdb\u884c\u6ce8\u91ca\u548c\u89e3\u91ca\u662f\u7406\u89e3\u5176\u751f\u7269\u5b66\u610f\u4e49\u7684\u5173\u952e\u6b65\u9aa4\u3002\u90a3\u5982\u4f55\u5b9e\u73b0\u5bf9\u4e0d\u540c\u53d8\u5f02\u7c7b\u578b\u7684\u6ce8\u91ca\u5462\uff1f<\/p>\n<p style=\"text-indent: 0em;text-wrap: wrap;\">\u76ee\u524d\uff0c\u6709\u8bb8\u591a\u5de5\u5177\u53ef\u4ee5\u7528\u6765\u6ce8\u91ca\u53d8\u5f02\uff0c\u4f46\u5176\u4e2d\u4e00\u4e2a\u6bd4\u8f83\u6d41\u884c\u548c\u5f3a\u5927\u7684\u662fsnpEFF\u3002snpEFF\u662f\u4e00\u4e2a\u5f00\u6e90\u7684Java\u7a0b\u5e8f\uff0c\u53ef\u4ee5\u5bf9VCF\u683c\u5f0f\u7684\u53d8\u5f02\u6587\u4ef6\u8fdb\u884c\u5feb\u901f\u548c\u51c6\u786e\u7684\u6ce8\u91ca\u3002snpEFF\u53ef\u4ee5\u9884\u6d4b\u53d8\u5f02\u5bf9\u8f6c\u5f55\u672c\u548c\u86cb\u767d\u8d28\u7684\u5f71\u54cd\uff0c\u4f8b\u5982\u9519\u4e49\u3001\u65e0\u4e49\u3001\u526a\u5207\u4f4d\u70b9\u3001\u542f\u52a8\u5b50\u3001\u7ec8\u6b62\u5b50\u7b49\u3002snpEFF\u8fd8\u53ef\u4ee5\u63d0\u4f9b\u5176\u4ed6\u6709\u7528\u7684\u4fe1\u606f\uff0c\u4f8b\u5982\u57fa\u56e0\u540d\u3001\u8f6c\u5f55\u672cID\u3001\u5916\u663e\u5b50\u7f16\u53f7\u3001\u5bc6\u7801\u5b50\u6539\u53d8\u3001\u6c28\u57fa\u9178\u6539\u53d8\u7b49\uff1bsnpEFF\u652f\u6301\u5305\u62ec\u4eba\u7c7b\u3001\u52a8\u7269\u3001\u690d\u7269\u3001\u5fae\u751f\u7269\u7b49\u8d85\u8fc738,000\u4e2a\u7269\u79cd\u7684\u57fa\u56e0\u7ec4\u6570\u636e\u5e93\uff0c\u4e5f\u53ef\u4ee5\u81ea\u5b9a\u4e49\u6570\u636e\u5e93\u6216\u4f7f\u7528\u516c\u5171\u6570\u636e\u5e93\u3002\u652f\u6301\u591a\u79cd\u53d8\u5f02\u683c\u5f0f\uff0c\u5305\u62ecVCF\u3001GFF\u3001BED\u7b49\uff1b\u652f\u6301\u591a\u79cd\u8f93\u51fa\u683c\u5f0f\uff0c\u5305\u62ec\u6587\u672c\u3001HTML\u3001VCF\u7b49\uff1b\u652f\u6301\u591a\u79cd\u7edf\u8ba1\u5206\u6790\uff0c\u5305\u62ec\u53d8\u5f02\u9891\u7387\u3001\u53d8\u5f02\u7c7b\u578b\u5206\u5e03\u3001\u53d8\u5f02\u529f\u80fd\u5206\u5e03\u7b49\u3002<\/p>\n<p style=\"text-indent: 0em;text-wrap: wrap;\">snpEFF\u7684\u4f7f\u7528\u975e\u5e38\u7b80\u5355\uff0c\u53ea\u9700\u8981\u51e0\u4e2a\u547d\u4ee4\u884c\u53c2\u6570\u5c31\u53ef\u4ee5\u8fd0\u884c\u3002snpEFF\u7684\u4f7f\u7528\u5305\u62ec\u4ee5\u4e0b\u51e0\u6b65\uff0c\u9996\u5148\u9700\u8981\u4e0b\u8f7dsnpEFF\u548c\u76f8\u5e94\u7684\u57fa\u56e0\u7ec4\u6570\u636e\u5e93\u6216\u8005\u81ea\u5b9a\u4e49\u6570\u636e\u5e93\u3002\u7136\u540e\u4f7f\u7528snpEff\u547d\u4ee4\u5bf9VCF\u6587\u4ef6\u8fdb\u884c\u6ce8\u91ca\uff0c\u6307\u5b9a\u6570\u636e\u5e93\u540d\u79f0\u548c\u8f93\u51fa\u6587\u4ef6\u540d\u3002\u6700\u540e\uff0c\u53ef\u4ee5\u4f7f\u7528snpEff\u7684\u4f34\u968f\u5de5\u5177SnpSift\u5bf9\u6ce8\u91ca\u7ed3\u679c\u8fdb\u884c\u8fc7\u6ee4\u3001\u6392\u5e8f\u6216\u7edf\u8ba1\u3002snpEFF\u8fd8\u53ef\u4ee5\u4e0e\u5176\u4ed6\u5de5\u5177\u96c6\u6210\uff0c\u4f8b\u5982GATK\u3001bcftools\u6216VEP\u3002<\/p>\n<\/section>\n<section style=\"text-align: left;justify-content: flex-start;margin: 20px 0%;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;min-width: 10%;flex: 0 0 auto;height: auto;background-color: rgb(204, 223, 237);border-width: 0px;border-radius: 0px 50px 50px 0px;border-style: none;border-color: rgb(62, 62, 62);padding-right: 10px;align-self: flex-start;\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;min-width: 10%;flex: 0 0 auto;height: auto;background-color: rgb(60, 86, 125);border-width: 0px;border-radius: 0px 50px 50px 0px;border-style: none;border-color: rgb(62, 62, 62);align-self: flex-start;\">\n<section style=\"color: rgb(255, 255, 254);line-height: 2;padding-right: 15px;padding-left: 15px;text-align: justify;\" powered-by=\"xiumi.us\">\n<p><strong>1. snpEFF\u7684\u4e0b\u8f7d\u4e0e\u5b89\u88c5<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p style=\"text-indent: 0em;text-wrap: wrap;\"><strong>\u65b9\u6cd5\u4e00\uff0c\u4e0b\u8f7d\u538b\u7f29\u5305\u5b89\u88c5\u3002<\/strong><span style=\"text-indent: 0em;\">\u4e0b\u8f7d\u7f51\u5740\uff1ahttps:\/\/sourceforge.net\/projects\/snpeff\/ <\/span><\/p>\n<p style=\"text-indent: 0em;text-wrap: wrap;\">\u4e0b\u8f7d\u89e3\u538b\u540e\uff0c\u4f1a\u5728snpEff\u6587\u4ef6\u5939\u4e2d\u751f\u4ea7\u4e24\u4e2ajar\u5305snpEff.jar\u548cSnpSift.jar\u3002\u8fd0\u884c\u547d\u4ee4java -jar snpEff.jar \u751f\u6210\u5e2e\u52a9\u6587\u4ef6\u5219\u5b89\u88c5\u6210\u529f\u3002<\/p>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.6351851851851852\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_YeARiaXhD3ic9bta9FtDTmNqXpFBIw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSNSNSA4ZJsgLwqzl7vCHyYhMGc3NHWNaIJ9zQmVr0iaAEoqhUYeARiaXhD3ic9bta9FtDTmNqXpFBIw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p><strong>\u65b9\u6cd5\u4e8c\uff0c\u4f7f\u7528conda\u5b89\u88c5snpEFF\u3002<\/strong><\/p>\n<p>conda\u662f\u53ef\u4ee5\u65b9\u4fbf\u5730\u5b89\u88c5\u548c\u66f4\u65b0\u5404\u79cd\u8f6f\u4ef6\u3002\u8981\u4f7f\u7528conda\u5b89\u88c5snpEFF\uff0c\u9996\u5148\u9700\u8981\u5b89\u88c5conda\uff0c\u53ef\u4ee5\u53c2\u8003\u5b98\u65b9\u7f51\u7ad9\u7684\u6559\u7a0b\uff1ahttps:\/\/docs.conda.io\/en\/latest\/miniconda.html \u3002\u5b89\u88c5\u597dconda\u540e\uff0c\u6253\u5f00\u7ec8\u7aef\uff0c\u8f93\u5165\u4ee5\u4e0b\u547d\u4ee4\uff1a<\/p>\n<p>conda install -c bioconda snpeff<\/p>\n<p>\u8fd9\u4e2a\u547d\u4ee4\u4f1a\u4ecebioconda\u9891\u9053\u4e0b\u8f7d\u5e76\u5b89\u88c5snpEFF\u53ca\u5176\u4f9d\u8d56\u7684\u8f6f\u4ef6\u5305\u3002\u5b89\u88c5\u5b8c\u6210\u540e\uff0c\u53ef\u4ee5\u4f7f\u7528\u4ee5\u4e0b\u547d\u4ee4\u68c0\u67e5snpEFF\u7684\u7248\u672c\uff1a<\/p>\n<p>snpeff -version<\/p>\n<p>\u5982\u679c\u663e\u793aSnpEff\u7248\u672c\u4fe1\u606f\uff0c\u8bf4\u660esnpEFF\u5df2\u7ecf\u6210\u529f\u5b89\u88c5\u3002<\/p>\n<\/section>\n<section style=\"text-align: left;justify-content: flex-start;margin: 20px 0%;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;min-width: 10%;flex: 0 0 auto;height: auto;background-color: rgb(204, 223, 237);border-width: 0px;border-radius: 0px 50px 50px 0px;border-style: none;border-color: rgb(62, 62, 62);padding-right: 10px;align-self: flex-start;\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;min-width: 10%;flex: 0 0 auto;height: auto;background-color: rgb(60, 86, 125);border-width: 0px;border-radius: 0px 50px 50px 0px;border-style: none;border-color: rgb(62, 62, 62);align-self: flex-start;\">\n<section style=\"color: rgb(255, 255, 254);line-height: 2;padding-right: 15px;padding-left: 15px;text-align: justify;\" powered-by=\"xiumi.us\">\n<p><strong>2. \u4e0b\u8f7d\u6216\u6784\u5efa\u6570\u636e\u5e93<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-indent: 0em;text-wrap: wrap;\"><strong>\u65b9\u6cd5\u4e00\uff1a\u4f7f\u7528snpEFF\u81ea\u5e26\u7684\u6570\u636e\u5e93<\/strong><\/p>\n<p style=\"text-indent: 0em;text-wrap: wrap;\">snpEFF\u81ea\u5e26\u4e86\u4e00\u4e9b\u5e38\u89c1\u7269\u79cd\u7684\u6570\u636e\u5e93\uff0c\u5982\u4eba\u7c7b\u3001\u5c0f\u9f20\u3001\u5927\u80a0\u6746\u83cc\u7b49\uff0c\u8fd9\u4e9b\u6570\u636e\u5e93\u53ef\u4ee5\u76f4\u63a5\u4e0b\u8f7d\u4f7f\u7528\u3002\u4e0b\u8f7d\u7684\u547d\u4ee4\u5982\u4e0b\uff1a<\/p>\n<p style=\"text-indent: 0em;text-wrap: wrap;\">java -jar snpEff.jar download -v hg19<\/p>\n<p style=\"text-indent: 0em;text-wrap: wrap;\">\u5176\u4e2dhg19\u662f\u4eba\u7c7b\u57fa\u56e0\u7ec4\u7684\u7248\u672c\u53f7\uff0c\u53ef\u4ee5\u6839\u636e\u9700\u8981\u66ff\u6362\u4e3a\u5176\u4ed6\u7269\u79cd\u548c\u7248\u672c\u3002\u4e0b\u8f7d\u5b8c\u6210\u540e\uff0c\u53ef\u4ee5\u5728snpEff\/data\u76ee\u5f55\u4e0b\u770b\u5230\u76f8\u5e94\u7684\u6587\u4ef6\u5939\uff0c\u91cc\u9762\u5305\u542b\u4e86\u57fa\u56e0\u7ec4\u5e8f\u5217\u548c\u6ce8\u91ca\u4fe1\u606f\u3002<\/p>\n<p style=\"text-indent: 0em;text-wrap: wrap;\"><strong>\u65b9\u6cd5\u4e8c\uff1a\u4f7f\u7528GFF3\u6216GTF\u6587\u4ef6\u5efa\u5e93<\/strong><\/p>\n<p style=\"text-indent: 0em;text-wrap: wrap;\">\u5982\u679csnpEFF\u6ca1\u6709\u63d0\u4f9b\u6240\u9700\u7269\u79cd\u7684\u6570\u636e\u5e93\uff0c\u6216\u8005\u9700\u8981\u4f7f\u7528\u81ea\u5df1\u7684\u6ce8\u91ca\u4fe1\u606f\uff0c\u53ef\u4ee5\u4f7f\u7528GFF3\u6216GTF\u6587\u4ef6\u6765\u5efa\u5e93\u3002\u8fd9\u4e9b\u6587\u4ef6\u53ef\u4ee5\u4ece\u5404\u79cd\u6570\u636e\u5e93\u6216\u7f51\u7ad9\u4e0b\u8f7d\uff0c\u4e5f\u53ef\u4ee5\u81ea\u5df1\u751f\u6210\u3002\u4f7f\u7528GFF3\u6216GTF\u6587\u4ef6\u5efa\u5e93\u7684\u547d\u4ee4\u5982\u4e0b\uff1a<\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">java -jar snpEff.jar build -<span class=\"code-snippet__built_in\">c<\/span> snpEff.config -gff3 -v my_genome<\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-indent: 0em;text-wrap: wrap;\" powered-by=\"xiumi.us\">\u5176\u4e2dmy_genome\u662f\u81ea\u5b9a\u4e49\u7684\u6570\u636e\u5e93\u540d\u79f0\uff0c\u53ef\u4ee5\u968f\u610f\u6307\u5b9a\u3002-c\u6307\u5b9a\u914d\u7f6e\u6587\u4ef6snpEff.config\uff0c-v\u6307\u5b9a\u5197\u957f\u6a21\u5f0f\u3002-gff3\u8868\u793a\u4f7f\u7528GFF3\u683c\u5f0f\u7684\u6587\u4ef6\uff0c\u5982\u679c\u662fGTF\u683c\u5f0f\uff0c\u5219\u6539\u4e3a-gtf\u3002\u5728\u6267\u884c\u547d\u4ee4\u4e4b\u524d\uff0c\u9700\u8981\u5148\u5728snpEff\/data\u76ee\u5f55\u4e0b\u521b\u5efa\u4e00\u4e2a\u4ee5my_genome\u4e3a\u540d\u7684\u6587\u4ef6\u5939\uff0c\u5e76\u5c06\u57fa\u56e0\u7ec4\u5e8f\u5217\u548cGFF3\u6216GTF\u6587\u4ef6\u653e\u5165\u5176\u4e2d\u3002\u57fa\u56e0\u7ec4\u5e8f\u5217\u5fc5\u987b\u547d\u540d\u4e3amy_genome.fa\uff0cGFF3\u6216GTF\u6587\u4ef6\u5fc5\u987b\u547d\u540d\u4e3agenes.gff\u6216genes.gtf\u3002\u5e76\u5728snpEff.config\u914d\u7f6e\u6587\u4ef6\u6700\u540e\u4e00\u884c\u52a0\u5165\uff1amy_genome.genome : my_genome\u3002<\/p>\n<section style=\"text-align: left;justify-content: flex-start;margin: 20px 0%;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;min-width: 10%;flex: 0 0 auto;height: auto;background-color: rgb(204, 223, 237);border-width: 0px;border-radius: 0px 50px 50px 0px;border-style: none;border-color: rgb(62, 62, 62);padding-right: 10px;align-self: flex-start;\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;min-width: 10%;flex: 0 0 auto;height: auto;background-color: rgb(60, 86, 125);border-width: 0px;border-radius: 0px 50px 50px 0px;border-style: none;border-color: rgb(62, 62, 62);align-self: flex-start;\">\n<section style=\"color: rgb(255, 255, 254);line-height: 2;padding-right: 15px;padding-left: 15px;text-align: justify;\" powered-by=\"xiumi.us\">\n<p><strong>3. snpEFF\u7684\u4f7f\u7528\u65b9\u6cd5<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p><strong>snpEFF\u7684\u57fa\u672c\u7528\u6cd5\u662f\uff1a<\/strong><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">java -jar snpEff.jar [options] genome_version input_file > output_file\u5176\u4e2d\uff1a- genome_version\uff1a<\/span><\/code><\/pre>\n<\/section>\n<section style=\"padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p>\u6307\u5b9a\u8981\u4f7f\u7528\u7684\u53c2\u8003\u57fa\u56e0\u7ec4\u548c\u6ce8\u91ca\u6570\u636e\u5e93\u7684\u7248\u672c\uff0c\u5982GRCh38.99\u3001hg19\u7b49\u3002\u53ef\u4ee5\u4f7f\u7528`java -jar snpEff.jar databases`\u547d\u4ee4\u67e5\u770b\u53ef\u7528\u7684\u6570\u636e\u5e93\u5217\u8868\u3002- input_file\uff1a\u6307\u5b9a\u8981\u6ce8\u91ca\u7684\u53d8\u5f02\u6587\u4ef6\uff0c\u53ef\u4ee5\u662fVCF\u3001GFF\u3001BED\u7b49\u683c\u5f0f\uff0c\u4e5f\u53ef\u4ee5\u662f\u6807\u51c6\u8f93\u5165\uff08stdin\uff09\u3002- output_file\uff1a\u6307\u5b9a\u8f93\u51fa\u6587\u4ef6\uff0c\u53ef\u4ee5\u662f\u6807\u51c6\u8f93\u51fa\uff08stdout\uff09\uff0c\u4e5f\u53ef\u4ee5\u662f\u4e00\u4e2a\u6587\u4ef6\u540d\u3002\u8f93\u51fa\u6587\u4ef6\u9ed8\u8ba4\u662fVCF\u683c\u5f0f\uff0c\u4e5f\u53ef\u4ee5\u901a\u8fc7\u53c2\u6570\u6307\u5b9a\u5176\u4ed6\u683c\u5f0f\u3002snpEFF\u7684\u5e38\u89c1\u53c2\u6570\u548c\u9009\u9879snpEFF\u6709\u5f88\u591a\u53c2\u6570\u548c\u9009\u9879\uff0c\u53ef\u4ee5\u6839\u636e\u9700\u8981\u8fdb\u884c\u8c03\u6574\u3002\u4ee5\u4e0b\u662f\u4e00\u4e9b\u5e38\u89c1\u7684\u53c2\u6570\u548c\u9009\u9879\uff1a- -v\uff1a\u663e\u793a\u8be6\u7ec6\u4fe1\u606f\uff0c\u5305\u62ec\u7a0b\u5e8f\u7248\u672c\u3001\u6570\u636e\u5e93\u7248\u672c\u3001\u8fd0\u884c\u65f6\u95f4\u7b49\u3002- -noLog\uff1a\u4e0d\u8f93\u51fa\u65e5\u5fd7\u4fe1\u606f\u3002- -noStats\uff1a\u4e0d\u8f93\u51fa\u7edf\u8ba1\u4fe1\u606f\u3002- -no-downstream\uff1a\u4e0d\u6ce8\u91ca\u4e0b\u6e38\u533a\u57df\uff08\u9ed8\u8ba4\u4e3a5kb\uff09\u7684\u53d8\u5f02\u3002- -no-upstream\uff1a\u4e0d\u6ce8\u91ca\u4e0a\u6e38\u533a\u57df\uff08\u9ed8\u8ba4\u4e3a5kb\uff09\u7684\u53d8\u5f02\u3002- -no-intergenic\uff1a\u4e0d\u6ce8\u91ca\u95f4\u57fa\u56e0\u533a\u57df\u7684\u53d8\u5f02\u3002- -no-intron\uff1a\u4e0d\u6ce8\u91ca\u5185\u542b\u5b50\u533a\u57df\u7684\u53d8\u5f02\u3002- -no-utr\uff1a\u4e0d\u6ce8\u91caUTR\u533a\u57df\u7684\u53d8\u5f02\u3002- -formatEff\uff1a\u8f93\u51fa\u683c\u5f0f\u4e3aEFF\u683c\u5f0f\uff0c\u800c\u4e0d\u662fVCF\u683c\u5f0f\u3002EFF\u683c\u5f0f\u662f\u4e00\u79cd\u7b80\u5316\u7684\u683c\u5f0f\uff0c\u53ea\u5305\u542b\u53d8\u5f02\u7684\u5f71\u54cd\u548c\u4e25\u91cd\u7a0b\u5ea6\u7b49\u4fe1\u606f\u3002- -csvStats\uff1a\u8f93\u51fa\u7edf\u8ba1\u4fe1\u606f\u4e3aCSV\u683c\u5f0f\uff0c\u800c\u4e0d\u662fHTML\u683c\u5f0f\u3002CSV\u683c\u5f0f\u65b9\u4fbf\u7528\u5176\u4ed6\u8f6f\u4ef6\u8fdb\u884c\u5206\u6790\u548c\u7ed8\u56fe\u3002<\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">\u793a\u4f8b\u547d\u4ee4\uff1a<\/span><\/code><code><span class=\"code-snippet_outer\">java -Xmx4G -jar snpEff.jar eff -csvStats variants.SnpEff.csv -s variants.SnpEff.html -<span class=\"code-snippet__built_in\">c<\/span> snpEff.config -v -ud <span class=\"code-snippet__number\">500<\/span> my_genome my_snp.vcf > my.SnpEff.vcf<\/span><\/code><\/pre>\n<\/section>\n<ul class=\"list-paddingleft-1\" style=\"padding-left: 40px;list-style-position: outside;\" powered-by=\"xiumi.us\">\n<li>\n<p>-Xmx2G\u6307\u5b9aJava\u865a\u62df\u673a\u7684\u6700\u5927\u5806\u5927\u5c0f\u4e3a4GB\u3002<\/p>\n<\/li>\n<li>\n<p>-csvStats variants.SnpEff.csv \u6307\u5b9a\u8f93\u51faCSV\u683c\u5f0f\u7684\u7edf\u8ba1\u4fe1\u606f\u3002<\/p>\n<\/li>\n<li>\n<p>-s variants.SnpEff.html \u6307\u5b9a\u8f93\u51faHTML\u683c\u5f0f\u7684\u6458\u8981\u62a5\u544a\u3002<\/p>\n<\/li>\n<li>\n<p>-ud 500\u6307\u5b9a\u4e0a\u6e38\/\u4e0b\u6e38\u533a\u95f4\u957f\u5ea6\u4e3a500\u4e2a\u78b1\u57fa\u3002<\/p>\n<\/li>\n<li>\n<p>my_genome \u6307\u5b9a\u8981\u4f7f\u7528\u7684\u57fa\u56e0\u7ec4\u3002<\/p>\n<\/li>\n<li>\n<p>my_snp.vcf \u6307\u5b9a\u8f93\u5165VCF\u6587\u4ef6\u3002<\/p>\n<\/li>\n<\/ul>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">\u7ed3\u675f\u540e\u5171\u8f93\u51fa<span class=\"code-snippet__number\">4<\/span>\u4e2a\u6587\u4ef6\uff1avariants.SnpEff.csv\u3001variants.SnpEff.html\u3001my.SnpEff.vcf\u3001my.SnpEff.genes.txt\u3002<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: left;justify-content: flex-start;margin: 20px 0%;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;min-width: 10%;flex: 0 0 auto;height: auto;background-color: rgb(204, 223, 237);border-width: 0px;border-radius: 0px 50px 50px 0px;border-style: none;border-color: rgb(62, 62, 62);padding-right: 10px;align-self: flex-start;\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;min-width: 10%;flex: 0 0 auto;height: auto;background-color: rgb(60, 86, 125);border-width: 0px;border-radius: 0px 50px 50px 0px;border-style: none;border-color: rgb(62, 62, 62);align-self: flex-start;\">\n<section style=\"color: rgb(255, 255, 254);line-height: 2;padding-right: 15px;padding-left: 15px;text-align: justify;\" powered-by=\"xiumi.us\">\n<p><strong>4. snpEFF\u6ce8\u91ca\u7ed3\u679c\u89e3\u8bfb<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p>HTML\u683c\u5f0f\u7684\u6458\u8981\u62a5\u544a\u662f\u4e00\u4e2a\u7f51\u9875\u6587\u4ef6\uff0c\u53ef\u4ee5\u7528\u6d4f\u89c8\u5668\u6253\u5f00\u3002\u5b83\u5305\u542b\u4e86\u4ee5\u4e0b\u51e0\u4e2a\u90e8\u5206\uff1a<\/p>\n<\/section>\n<ul style=\"list-style-type: \uf0b7;padding-left: 40px;list-style-position: outside;\" class=\"list-paddingleft-1\" powered-by=\"xiumi.us\">\n<li>\n<p>Summary\uff1a\u8fd9\u90e8\u5206\u663e\u793a\u4e86\u4e00\u4e9b\u57fa\u672c\u7684\u4fe1\u606f\uff0c\u5982\u57fa\u56e0\u7ec4\u540d\u79f0\u3001\u6ce8\u91ca\u65e5\u671f\u3001\u6ce8\u91ca\u547d\u4ee4\u3001\u8b66\u544a\u4fe1\u606f\u3001\u9519\u8bef\u4fe1\u606f\u3001\u8f93\u5165\u6587\u4ef6\u884c\u6570\u3001\u53d8\u5f02\u4f4d\u70b9\u6570\uff08\u8fc7\u6ee4\u524d\u540e\uff09\u3001\u975e\u53d8\u5f02\u4f4d\u70b9\u6570\u3001\u5177\u6709ID\u7684\u53d8\u5f02\u4f4d\u70b9\u6570\u3001\u975e\u53cc\u7b49\u4f4d\u57fa\u56e0\u7ec4SNP\u4f4d\u70b9\u6570\u3001Number of effects\u3001\u53c2\u8003\u57fa\u56e0\u7ec4\u603b\u957f\u5ea6\u3001\u53c2\u8003\u57fa\u56e0\u7ec4\u6709\u6548\u957f\u5ea6\u3001\u53d8\u5f02\u7387\u7b49\u3002<\/p>\n<\/li>\n<\/ul>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.4462962962962963\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-09-20_\u300c\u8f6c\u300dSnpEff\uff1a\u4e00\u4e2a\u795e\u5947\u7684\u57fa\u56e0\u7ec4\u53d8\u5f02\u6ce8\u91ca\u5de5\u5177\/2_oicMr4Oe0BM8FKG37nIdniafnIv63Q.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSNSNSA4ZJsgLwqzl7vCHyYPp4UIRiaUiadnoG34xt9WNTCMKh6oicMr4Oe0BM8FKG37nIdniafnIv63Q\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section style=\"padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<ul style=\"list-style-type: \uf0b7;padding-left: 40px;list-style-position: outside;\" class=\"list-paddingleft-1\">\n<li>\n<p>Variant types\uff1a\u8fd9\u90e8\u5206\u663e\u793a\u4e86\u4e0d\u540c\u7c7b\u578b\u7684\u53d8\u5f02\u7684\u6570\u91cf\u548c\u767e\u5206\u6bd4\uff0c\u5305\u62ecSNP\uff08\u5355\u6838\u82f7\u9178\u591a\u6001\u6027\uff09\u3001MNP\uff08\u591a\u6838\u82f7\u9178\u591a\u6001\u6027\uff09\u3001INS\uff08\u63d2\u5165\u53d8\u5f02\uff09\u3001DEL\uff08\u7f3a\u5931\u53d8\u5f02\uff09\u3001MIXED\uff08\u6df7\u5408\u53d8\u5f02\uff09\u3001INV (\u5012\u4f4d\u53d8\u5f02\uff09\u3001DUP\uff08\u91cd\u590d\u53d8\u5f02\uff09\u3001BED\uff08\u6613\u4f4d\u53d8\u5f02\uff09\u3001INTERVAL\uff08\u95f4\u9694\u53d8\u5f02\uff09\u7b49\u3002<\/p>\n<\/li>\n<\/ul>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.3285198555956679\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-09-20_\u300c\u8f6c\u300dSnpEff\uff1a\u4e00\u4e2a\u795e\u5947\u7684\u57fa\u56e0\u7ec4\u53d8\u5f02\u6ce8\u91ca\u5de5\u5177\/3_eIOmnyMjO6pfTvmAkHUqpxCnq7HeYw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSNSNSA4ZJsgLwqzl7vCHyYFXW3iboUmR2tvT6hf4qh9qoLxeIOmnyMjO6pfTvmAkHUqpxCnq7HeYw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"277\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section style=\"padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<ul style=\"list-style-type: \uf0b7;padding-left: 40px;list-style-position: outside;\" class=\"list-paddingleft-1\">\n<li>\n<p>Effects by type\uff1a\u8fd9\u90e8\u5206\u663e\u793a\u4e86\u4e0d\u540c\u7c7b\u578b\u7684\u6548\u5e94\u7684\u6570\u91cf\u548c\u767e\u5206\u6bd4\uff0c\u5305\u62ec3\u2019\u7aef\u4e3b\u8981UTR\u53d8\u5f02\u30015\u2019\u7aef\u4e3b\u8981UTR\u63d0\u524d\u542f\u52a8\u5b50\u83b7\u5f97\u53d8\u5f02\u30015\u2019\u7aef\u4e3b\u8981UTR\u53d8\u5f02\u3001\u4e0b\u6e38\u57fa\u56e0\u53d8\u5f02\u3001\u8d77\u59cb\u5bc6\u7801\u5b50\u7f16\u7801\u53d8\u5f02\u3001\u57fa\u56e0\u95f4\u9694\u533a\u3001\u5185\u542b\u5b50\u53d8\u5f02\u3001\u526a\u63a5\u53d7\u4f53\u53d8\u5f02\u3001\u526a\u63a5\u4f9b\u4f53\u53d8\u5f02\u3001\u526a\u63a5\u533a\u57df\u53d8\u5f02\u3001\u8d77\u59cb\u7f3a\u5931\u3001\u8d77\u59cb\u4fdd\u7559\u53d8\u5f02\u3001\u7ec8\u6b62\u83b7\u5f97\u3001\u7ec8\u6b62\u7f3a\u5931\u3001\u7ec8\u6b62\u4fdd\u7559\u53d8\u5f02\u3001\u540c\u4e49\u53d8\u5f02\u3001\u4e0a\u6e38\u57fa\u56e0\u53d8\u5f02\u7b49\u3002<\/p>\n<\/li>\n<li>\n<p>Effects by region\uff1a\u8fd9\u90e8\u5206\u663e\u793a\u4e86\u4e0d\u540c\u533a\u57df\u7684\u6548\u5e94\u7684\u6570\u91cf\u548c\u767e\u5206\u6bd4\uff0c\u5305\u62ec\u4e0b\u6e38\u3001\u5916\u663e\u5b50\u3001\u95f4\u9694\u533a\u3001\u5185\u542b\u5b50\u3001\u526a\u63a5\u4f4d\u70b9\u53d7\u4f53\u3001\u526a\u63a5\u4f4d\u70b9\u4f9b\u4f53\u3001\u526a\u63a5\u4f4d\u70b9\u533a\u57df\u3001\u4e0a\u6e38\u30013\u2019UTR\u533a\u30015\u2019UTR\u533a\u7b49\u3002<\/p>\n<\/li>\n<\/ul>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.5972222222222222\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_W8Ey8VWJgqXicbBIFxlw0kWluf4Y6g.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSNSNSA4ZJsgLwqzl7vCHyYeC93eHiaeLmFV2Yb0bbKSHewACW8Ey8VWJgqXicbBIFxlw0kWluf4Y6g\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.3805970149253731\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-09-20_\u300c\u8f6c\u300dSnpEff\uff1a\u4e00\u4e2a\u795e\u5947\u7684\u57fa\u56e0\u7ec4\u53d8\u5f02\u6ce8\u91ca\u5de5\u5177\/5_BA8u0fT99L1pReECmzicwy1jrKfbvQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSNSNSA4ZJsgLwqzl7vCHyYfzxt1mMpEqsFu6IS6URRxPxS1BA8u0fT99L1pReECmzicwy1jrKfbvQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"938\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<ul style=\"list-style-type: \uf0b7;padding-left: 40px;list-style-position: outside;\" class=\"list-paddingleft-1\" powered-by=\"xiumi.us\">\n<li>\n<p>Effects by functional class\uff1a\u8fd9\u90e8\u5206\u663e\u793a\u4e86\u4e0d\u540c\u529f\u80fd\u7c7b\u522b\u7684\u6548\u5e94\u7684\u6570\u91cf\u548c\u767e\u5206\u6bd4\uff0c\u5305\u62ec\u65e0\u6548\u679c\uff08NONE\uff09\u3001\u4fee\u9970\u6027\uff08MODIFIER\uff09\u3001\u4f4e\u5f71\u54cd\uff08LOW\uff09\u3001\u4e2d\u7b49\u5f71\u54cd\uff08MODERATE\uff09\u3001\u9ad8\u5f71\u54cd\uff08HIGH\uff09\u7b49\u3002<\/p>\n<\/li>\n<\/ul>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.38571428571428573\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-09-20_\u300c\u8f6c\u300dSnpEff\uff1a\u4e00\u4e2a\u795e\u5947\u7684\u57fa\u56e0\u7ec4\u53d8\u5f02\u6ce8\u91ca\u5de5\u5177\/6_vgCibGLhia3sr6F5p2c0KGJ2mom1mQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSNSNSA4ZJsgLwqzl7vCHyYn4ItGJ1SwZtuZw7j4pYibq4b69ZvgCibGLhia3sr6F5p2c0KGJ2mom1mQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"420\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<ul style=\"list-style-type: \uf0b7;padding-left: 40px;list-style-position: outside;\" class=\"list-paddingleft-1\" powered-by=\"xiumi.us\">\n<li>\n<p>Transitions \/ Transversions\uff1a\u8fd9\u90e8\u5206\u663e\u793a\u4e86\u8f6c\u6362\/\u98a0\u6362\u7684\u6bd4\u4f8b\u548c\u6570\u91cf\uff0c\u4ee5\u53ca\u4e0d\u540c\u7c7b\u578b\u7684\u8f6c\u6362\/\u98a0\u6362\u7684\u6570\u91cf\u548c\u767e\u5206\u6bd4\u3002\u8f6c\u6362\u662f\u6307\u560c\u5464\u4e0e\u560c\u5464\u6216\u5627\u5576\u4e0e\u5627\u5576\u4e4b\u95f4\u7684\u66ff\u4ee3\uff0c\u98a0\u6362\u662f\u6307\u560c\u5464\u4e0e\u5627\u5576\u4e4b\u95f4\u7684\u66ff\u4ee3\u3002<\/p>\n<\/li>\n<\/ul>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.39299610894941633\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_piaxOvoEKtW2icgicGCmuRsB8MqvtA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSNSNSA4ZJsgLwqzl7vCHyYyngmsTyWgwVNvXUXfWGRwBEh8ZJpiaxOvoEKtW2icgicGCmuRsB8MqvtA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"257\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<ul style=\"list-style-type: \uf0b7;padding-left: 40px;list-style-position: outside;\" class=\"list-paddingleft-1\" powered-by=\"xiumi.us\">\n<li>\n<p>Allele frequency histogram\uff1a\u8fd9\u90e8\u5206\u663e\u793a\u4e86\u7b49\u4f4d\u57fa\u56e0\u9891\u7387\u7684\u76f4\u65b9\u56fe\uff0c\u6a2a\u5750\u6807\u4e3a\u7b49\u4f4d\u57fa\u56e0\u9891\u7387\uff0c\u7eb5\u5750\u6807\u4e3a\u6570\u91cf\u3002<\/p>\n<\/li>\n<li>\n<p>Allele count histogram\uff1a\u8fd9\u90e8\u5206\u663e\u793a\u4e86\u7b49\u4f4d\u57fa\u56e0\u6570\u91cf\u7684\u76f4\u65b9\u56fe\uff0c\u6a2a\u5750\u6807\u4e3a\u7b49\u4f4d\u57fa\u56e0\u6570\u91cf\uff0c\u7eb5\u5750\u6807\u4e3a\u6570\u91cf\u3002<\/p>\n<\/li>\n<li>\n<p>Genotype summary\uff1a\u8fd9\u90e8\u5206\u663e\u793a\u4e86\u6837\u672c\u57fa\u56e0\u578b\u7684\u6c47\u603b\u4fe1\u606f\uff0c\u5305\u62ec\u6742\u5408\u57fa\u56e0\u578b\uff08HETEROZYGOUS\uff09\u3001\u7eaf\u5408\u57fa\u56e0\u578b\uff08HOMOZYGOUS\uff09\u3001\u7f3a\u5931\u57fa\u56e0\u578b\uff08MISSING\uff09\u7b49\u3002<\/p>\n<\/li>\n<li>\n<p>Codon change histogram\uff1a\u8fd9\u90e8\u5206\u663e\u793a\u4e86\u5bc6\u7801\u5b50\u6539\u53d8\u7684\u76f4\u65b9\u56fe\uff0c\u6a2a\u5750\u6807\u4e3a\u5bc6\u7801\u5b50\u6539\u53d8\u7c7b\u578b\uff0c\u7eb5\u5750\u6807\u4e3a\u6570\u91cf\u3002\u5bc6\u7801\u5b50\u6539\u53d8\u662f\u6307\u5355\u6838\u82f7\u9178\u7a81\u53d8\u5bfc\u81f4\u5bc6\u7801\u5b50\u53d1\u751f\u6539\u53d8\u3002<\/p>\n<\/li>\n<li>\n<p>Amino acid change histogram\uff1a\u8fd9\u90e8\u5206\u663e\u793a\u4e86\u6c28\u57fa\u9178\u6539\u53d8\u7684\u76f4\u65b9\u56fe\uff0c\u6a2a\u5750\u6807\u4e3a\u6c28\u57fa\u9178\u6539\u53d8\u7c7b\u578b\uff0c\u7eb5\u5750\u6807\u4e3a\u6570\u91cf\u3002\u6c28\u57fa\u9178\u6539\u53d8\u662f\u6307\u5355\u6838\u82f7\u9178\u7a81\u53d8\u5bfc\u81f4\u5bc6\u7801\u5b50\u53d1\u751f\u6539\u53d8\uff0c\u8fdb\u800c\u5bfc\u81f4\u6c28\u57fa\u9178\u53d1\u751f\u6539\u53d8\uff08\u9519\u4e49\u7a81\u53d8\uff09\u3002<\/p>\n<\/li>\n<li>\n<p>Chromosome summary\uff1a\u8fd9\u90e8\u5206\u663e\u793a\u4e86\u67d3\u8272\u4f53\u7684\u6c47\u603b\u4fe1\u606f\uff0c\u5305\u62ec\u67d3\u8272\u4f53\u540d\u79f0\u3001\u53c2\u8003\u57fa\u56e0\u7ec4\u957f\u5ea6\u3001\u6709\u6548\u957f\u5ea6\u3001\u53d8\u5f02\u4f4d\u70b9\u6570\u3001\u53d8\u5f02\u7387\u7b49\u3002<\/p>\n<\/li>\n<\/ul>\n<p style=\"text-indent: 0em;text-wrap: wrap;\" powered-by=\"xiumi.us\">snpEFF\u662f\u4e00\u4e2a\u975e\u5e38\u5f3a\u5927\u800c\u53c8\u65b9\u4fbf\u7684\u6ce8\u91ca\u5de5\u5177\uff0c\u6211\u5f3a\u70c8\u63a8\u8350\u5927\u5bb6\u5c1d\u8bd5\u4e00\u4e0b\u3002\u5982\u679c\u4f60\u60f3\u4e86\u89e3\u66f4\u591a\u5173\u4e8esnpEFF\u7684\u4fe1\u606f\uff0c\u4f60\u53ef\u4ee5\u8bbf\u95ee\u5b83\u7684\u5b98\u7f51\uff1ahttp:\/\/snpeff.sourceforge.net\/\u3002\u5982\u679c\u4f60\u6709\u4efb\u4f55\u5173\u4e8esnpEFF\u7684\u95ee\u9898\u6216\u5efa\u8bae\uff0c\u4f60\u53ef\u4ee5\u5728\u8bc4\u8bba\u533a\u7559\u8a00\uff0c\u6211\u4f1a\u5c3d\u5feb\u56de\u590d\u4f60\u3002\u8c22\u8c22\u5927\u5bb6\u7684\u9605\u8bfb\uff0c\u4e0b\u6b21\u518d\u89c1\uff01<\/p>\n<section style=\"margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"box-shadow: rgb(170, 170, 170) 0px 0px 10px inset;border-color: rgb(192, 200, 209);padding: 10px;border-width: 1px;border-style: solid;background-color: rgb(250, 250, 239);\">\n<section style=\"color: rgb(51, 51, 51);text-align: center;padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p style=\"text-align: justify;text-wrap: wrap;\">\u5927\u6d77\u54e5\u4eca\u5929\u7684\u8bb2\u89e3\u5c31\u5230\u8fd9\u91cc\u4e86~\u4e0b\u671f\u6211\u5c06\u4f1a\u5e26\u6765\u5bf9\u5355\u7ec6\u80de\u6d4b\u5e8f\u5206\u6790\u7ed3\u679c\u7684\u89e3\u8bfb~\u6211\u4eec\u4e0d\u89c1\u4e0d\u6563<\/p>\n<p style=\"text-align: justify;text-wrap: wrap;\">\uff08\u6700\u540e\u63a8\u8350\u4e00\u4e0b\u5927\u6d77\u54e5\u65b0\u5f00\u53d1\u7684\u96f6\u4ee3\u7801\u4e91\u751f\u4fe1\u5206\u6790\u5de5\u5177\u5e73\u53f0\u5305\u542b\u8d85\u591a\u96f6\u4ee3\u7801\u5c0f\u5de5\u5177\uff0c\u4e0a\u4f20\u6570\u636e\u4e00\u952e\u51fa\u56fe\uff0c\u611f\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u6b22\u8fce\u6765\u53c2\u89c2\u54df\u3002<\/p>\n<p style=\"text-align: justify;text-wrap: wrap;\">\u7f51\u5740\uff1a<\/p>\n<p style=\"text-align: justify;text-wrap: wrap;\">http:\/\/www.biocloudservice.com\/home.html\uff09<\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"text-align: center;justify-content: center;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: auto;align-self: center;flex: 0 0 auto;min-width: 5%;height: auto;\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;margin-left: -6px;\">\n<section style=\"transform: rotateZ(45deg);\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;\">\n<section style=\"display: inline-block;width: 16px;height: 16px;vertical-align: top;overflow: hidden;border-style: solid;border-width: 3px 3px 0px 0px;border-color: rgb(231, 215, 173) rgb(231, 215, 173) rgb(69, 107, 176) rgb(69, 107, 176);\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;margin-left: -6px;\">\n<section style=\"transform: rotateZ(45deg);\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;\">\n<section style=\"display: inline-block;width: 16px;height: 16px;vertical-align: top;overflow: hidden;border-style: solid;border-width: 3px 3px 0px 0px;border-color: rgb(231, 215, 173) rgb(231, 215, 173) rgb(69, 107, 176) rgb(69, 107, 176);\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;margin-left: -6px;\">\n<section style=\"transform: rotateZ(45deg);\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;\">\n<section style=\"display: inline-block;width: 16px;height: 16px;vertical-align: top;overflow: hidden;border-style: solid;border-width: 3px 3px 0px 0px;border-color: rgb(231, 215, 173) rgb(231, 215, 173) rgb(69, 107, 176) rgb(69, 107, 176);\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: 38%;align-self: center;flex: 0 0 auto;height: auto;padding: 3px 23px;\">\n<section style=\"line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.025925925925926\" data-s=\"300,640\" 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