{"id":1554,"date":"2025-05-07T11:27:28","date_gmt":"2025-05-07T03:27:28","guid":{"rendered":"http:\/\/www.majunpeng.com\/?p=1554"},"modified":"2025-06-10T20:45:28","modified_gmt":"2025-06-10T12:45:28","slug":"annovar%e5%af%b9vcf%e8%bf%9b%e8%a1%8c%e6%b3%a8%e9%87%8a","status":"publish","type":"post","link":"http:\/\/www.majunpeng.com\/index.php\/2025\/05\/07\/annovar%e5%af%b9vcf%e8%bf%9b%e8%a1%8c%e6%b3%a8%e9%87%8a\/","title":{"rendered":"ANNOVAR\u5bf9VCF\u8fdb\u884c\u6ce8\u91ca"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-post\" data-elementor-id=\"1554\" class=\"elementor elementor-1554\" data-elementor-post-type=\"post\">\n\t\t\t\t<div class=\"elementor-element elementor-element-6e4aa78 e-flex e-con-boxed e-con e-parent\" data-id=\"6e4aa78\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-72b8cba elementor-widget elementor-widget-heading\" data-id=\"72b8cba\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">1. \u524d\u8a00<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-4d0713a elementor-widget elementor-widget-text-editor\" data-id=\"4d0713a\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u901a\u8fc7Pggb\u505a\u5b8c\u4e86\u56fe\u6cdb\u7684\u6784\u5efa\uff0c\u63a5\u4e0b\u6765\u5c31\u8981\u627e\u5230\u5173\u952e\u57fa\u56e0\u7684SV\uff0c\u56e0\u6b64\u4f7f\u7528ANNOVAR\u6765\u5b8c\u6210\u8fd9\u9879\u5de5\u4f5c\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-8ec42a3 elementor-widget elementor-widget-heading\" data-id=\"8ec42a3\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">2. \u8f6f\u4ef6\u4e0b\u8f7d<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-ec2b1ef elementor-widget elementor-widget-text-editor\" data-id=\"ec2b1ef\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>ANNOVAR\u4e0b\u8f7d\u9700\u8981\u901a\u8fc7\u5b98\u65b9\u6587\u6863\u63d0\u4ea4\u6ce8\u518c\u4fe1\u606f\uff0c\u7136\u540e\u4f1a\u901a\u8fc7\u90ae\u4ef6\u53d1\u9001\u8f6f\u4ef6\u7684\u4e0b\u8f7d\u5730\u5740\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-d12e356 elementor-widget elementor-widget-text-editor\" data-id=\"d12e356\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u4e0b\u8f7d\u8f6c\u6362\u683c\u5f0f\u9700\u8981\u7684gtftogenepred\u8f6f\u4ef6<\/p><p>mamba install bioconda::ucsc-gtftogenepred<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-7ec82f9 elementor-widget elementor-widget-heading\" data-id=\"7ec82f9\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">3. \u51c6\u5907\u8f93\u5165\u6587\u4ef6<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-19e6f93 elementor-widget elementor-widget-text-editor\" data-id=\"19e6f93\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u56e0\u4e3a\u6211\u505a\u7684\u662f\u975e\u6a21\u5f0f\u7269\u79cd\u7684Vcf\u6ce8\u91ca\uff0c\u6240\u4ee5\u8981\u81ea\u5df1\u6784\u5efa\u6570\u636e\u5e93<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-c149a24 elementor-widget elementor-widget-html\" data-id=\"c149a24\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"html.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<p>gtfToGenePred -genePredExt Arabidopsis_thaliana.TAIR10.27.gtf AT_refGene.txt<\/p>\r\n<p># -genePredExt \u57fa\u56e0\u7ec4\u6ce8\u91cagtf\u6587\u4ef6<\/p>\r\n<p><\/p>\r\n<p>perl retrieve_seq_from_fasta.pl --format refGene --seqfile Arabidopsis_thaliana.TAIR10.27.dna.genome.fa AT_refGene.txt -outfile AT_refGeneMrna.fa<\/p>\r\n<p># --format \u6307\u5b9a\u683c\u5f0f<\/p>\r\n<p># --seqfile \u57fa\u56e0\u7ec4\u6587\u4ef6<\/p>\r\n<p># -outfile \u8f93\u51fa\u7684\u6570\u636e\u5e93\u6587\u4ef6<\/p>\r\n<p><\/p>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-c2164b2 elementor-widget elementor-widget-text-editor\" data-id=\"c2164b2\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u901a\u8fc7\u4e0a\u9762\u6b65\u9aa4\uff0c\u6700\u540e\u4f1a\u751f\u6210\u4e86\uff081\uff09AT_refGene.txt\uff082\uff09AT_refGeneMrna.fa\u8fd9\u4e24\u4e2a\u6570\u636e\u5e93\u6587\u4ef6\uff0c\u662f\u540e\u7eed\u5206\u6790\u9700\u8981\u7528\u5230\u7684\u3002\u6b64\u5916\uff0cANNOCAR\u8981\u6c42\u8f93\u5165\u7684\u53d8\u5f02\u6587\u4ef6\u4e0d\u662fvcf\u683c\u5f0f\u63a5\u4e0b\u6765\u53ea\u9700\u8981\u5bf9vcf\u6587\u4ef6\u8fdb\u884c\u683c\u5f0f\u8f6c\u6362\u5373\u53ef\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-49f815c elementor-widget elementor-widget-code-highlight\" data-id=\"49f815c\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-javascript line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-javascript\">\n\t\t\t\t\t<xmp>perl ~\/Software\/annovar\/convert2annovar.pl -format vcf4old ..\/Total_vcf\/Chr_1.vcf > Chr_1.avinput<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-32b1705 elementor-widget elementor-widget-heading\" data-id=\"32b1705\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">4. \u8fd0\u884c\u6ce8\u91ca<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-96804a3 elementor-widget elementor-widget-code-highlight\" data-id=\"96804a3\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-bash line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-bash\">\n\t\t\t\t\t<xmp>perl ~\/Software\/annovar\/annotate_variation.pl -geneanno -dbtype refGene -out Test_change -build Chrysanthemum_rhombifolium Chr_1_change.avinput .\/\n\n# -geneanno \u6307\u5b9a\u6ce8\u91ca\u7c7b\u578b\n\n# -dbtype \u6570\u636e\u5e93\u7c7b\u578b\n\n# -out \u8f93\u51fa\u7ed3\u679c\u524d\u7f00\n\n#-build \u6784\u5efa\u7684\u6570\u636e\u5e93\u6587\u4ef6\u7684\u524d\u7f00\n\n# .\/ \u6570\u636e\u5e93\u6587\u4ef6\u7684\u8def\u5f84\uff0c\u8fd9\u91cc\u9700\u8981\u6ce8\u610f\u7684\u662f\uff0c\u4e00\u5b9a\u8981\u662f\u548c\u4e0a\u8fb9\u6784\u5efa\u7684\u524d\u7f00\u80fd\u5bf9\u4e0a\u3002\u4f8b\u59821\uff09AT_refGene.txt\uff082\uff09AT_refGeneMrna.fa\u7684\u524d\u7f00\u5c31\u662fAT<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-f3736d5 elementor-widget elementor-widget-heading\" data-id=\"f3736d5\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">5. \u8f93\u51fa\u7ed3\u679c<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-541f785 elementor-widget elementor-widget-text-editor\" data-id=\"541f785\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u8f93\u51fa\u7ed3\u679c\u6bd4\u8f83\u6709\u7528\u7684\u5c31\u662f.variant_function\uff0c\u683c\u5f0f\u5982\u4e0b<\/p><p>\u7b2c\u4e00\u5217\uff1a\u6ce8\u91ca\u7c7b\u578b<\/p><p>\u7b2c\u4e8c\u5217\uff1a\u53d8\u5f02\u6240\u5728\u7684\u57fa\u56e0<\/p><p>\u7b2c\u4e09\u5217\uff1a\u67d3\u8272\u4f53<\/p><p>\u7b2c\u56db\u5217\u548c\u7b2c\u4e94\u5217\uff1a\u8d77\u59cb\u4f4d\u7f6e\u548c\u7ec8\u6b62\u4f4d\u7f6e<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-93cdbce elementor-widget elementor-widget-code-highlight\" data-id=\"93cdbce\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-default copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-javascript line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-javascript\">\n\t\t\t\t\t<xmp>intergenic      evm.TU.Chr1.2(dist=1573),evm.TU.Chr1.3(dist=5608)       Chr1    21438   21438   C       T       unknown 60\nintergenic      evm.TU.Chr1.2(dist=1600),evm.TU.Chr1.3(dist=5581)       Chr1    21465   21465   T       A       unknown 60\nintergenic      evm.TU.Chr1.2(dist=1604),evm.TU.Chr1.3(dist=5577)       Chr1    21469   21469   C       T       unknown 60\nintergenic      evm.TU.Chr1.2(dist=1609),evm.TU.Chr1.3(dist=5572)       Chr1    21474   21474   C       T       unknown 60\nintergenic      evm.TU.Chr1.2(dist=1618),evm.TU.Chr1.3(dist=5563)       Chr1    21483   21483   T       A       unknown 60\nintergenic      evm.TU.Chr1.2(dist=1621),evm.TU.Chr1.3(dist=5560)       Chr1    21486   21486   T       A       unknown 60\nintergenic      evm.TU.Chr1.2(dist=1629),evm.TU.Chr1.3(dist=5552)       Chr1    21494   21494   T       C       unknown 60\nintergenic      evm.TU.Chr1.2(dist=1650),evm.TU.Chr1.3(dist=5531)       Chr1    21515   21515   T       A       unknown 60\nintergenic      evm.TU.Chr1.2(dist=1654),evm.TU.Chr1.3(dist=5527)       Chr1    21519   21519   C       T       unknown 60\nintergenic      evm.TU.Chr1.2(dist=1659),evm.TU.Chr1.3(dist=5521)       Chr1    21524   21525   TT      CA      unknown 60<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"<p>1. \u524d\u8a00 \u901a\u8fc7Pggb\u505a\u5b8c\u4e86\u56fe\u6cdb\u7684\u6784\u5efa\uff0c\u63a5\u4e0b\u6765\u5c31\u8981\u627e\u5230\u5173\u952e\u57fa\u56e0\u7684SV\uff0c\u56e0\u6b64\u4f7f\u7528ANNOVAR\u6765\u5b8c\u6210\u8fd9\u9879\u5de5\u4f5c\u3002 &#8230; <a title=\"ANNOVAR\u5bf9VCF\u8fdb\u884c\u6ce8\u91ca\" class=\"read-more\" href=\"http:\/\/www.majunpeng.com\/index.php\/2025\/05\/07\/annovar%e5%af%b9vcf%e8%bf%9b%e8%a1%8c%e6%b3%a8%e9%87%8a\/\" aria-label=\"\u9605\u8bfb ANNOVAR\u5bf9VCF\u8fdb\u884c\u6ce8\u91ca\">\u9605\u8bfb\u66f4\u591a<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_crdt_document":"","footnotes":""},"categories":[6],"tags":[],"class_list":["post-1554","post","type-post","status-publish","format-standard","hentry","category-6"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v23.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>ANNOVAR\u5bf9VCF\u8fdb\u884c\u6ce8\u91ca - \u5c0f\u9a6c\u751f\u4fe1\u65e5\u8bb0<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" 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