{"id":1641,"date":"2025-06-11T16:19:56","date_gmt":"2025-06-11T08:19:56","guid":{"rendered":"http:\/\/www.majunpeng.com\/?p=1641"},"modified":"2025-06-13T16:03:57","modified_gmt":"2025-06-13T08:03:57","slug":"vcf%e6%96%87%e4%bb%b6%e4%b8%ad%e7%ad%9b%e9%80%89sv","status":"publish","type":"post","link":"http:\/\/www.majunpeng.com\/index.php\/2025\/06\/11\/vcf%e6%96%87%e4%bb%b6%e4%b8%ad%e7%ad%9b%e9%80%89sv\/","title":{"rendered":"VCF\u6587\u4ef6\u4e2d\u7b5b\u9009SV"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-post\" data-elementor-id=\"1641\" class=\"elementor elementor-1641\" data-elementor-post-type=\"post\">\n\t\t\t\t<div class=\"elementor-element elementor-element-ad75fbb e-flex e-con-boxed e-con e-parent\" data-id=\"ad75fbb\" 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-b47f732 elementor-widget elementor-widget-heading\" data-id=\"b47f732\" 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-f49e3b2 elementor-widget elementor-widget-text-editor\" data-id=\"f49e3b2\" 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>Pggb\u8f93\u51fa\u7684VCF\u6587\u4ef6\u9664\u4e86\u6709SV\u8fd8\u6709SNP\uff0c\u56e0\u6b64\u8981\u628aSV\u5355\u72ec\u63d0\u53d6\u51fa\u6765\uff0c\u540e\u7eed\u6240\u6709\u7684\u5206\u6790\u90fd\u662f\u57fa\u4e8eSV\u7684\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-8af8b70 elementor-widget elementor-widget-heading\" data-id=\"8af8b70\" 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\u5b89\u88c5<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-25277fa elementor-widget elementor-widget-code-highlight\" data-id=\"25277fa\" 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>mamba create -n Truvari\nmamba activate Truvari\npython3 -m pip install Truvari <\/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-26eee49 elementor-widget elementor-widget-heading\" data-id=\"26eee49\" 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. \u8fd0\u884c<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-fdc132d elementor-widget elementor-widget-heading\" data-id=\"fdc132d\" 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<h3 class=\"elementor-heading-title elementor-size-default\">3.1 \u9274\u5b9aSV\u7c7b\u578b\u548c\u957f\u5ea6<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-7ea8adb elementor-widget elementor-widget-code-highlight\" data-id=\"7ea8adb\" 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>truvari anno svinfo -o SV_Chr_1.vcf Chr_1.vcf<\/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-90163f5 elementor-widget elementor-widget-heading\" data-id=\"90163f5\" 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<h3 class=\"elementor-heading-title elementor-size-default\">3.2 \u63d0\u53d6SV<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-3865249 elementor-widget elementor-widget-code-highlight\" data-id=\"3865249\" 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>bcftools view -i 'SVTYPE=\"DEL\" || SVTYPE=\"INS\"' SV_Chr_1.vcf -o SV_Chr_1_DEL_INS.vcf\nbcftools view -i 'SVTYPE=\"DEL\"' SV_Chr_1.vcf -o SV_Chr_1_DEL.vcf\nbcftools view -i 'SVTYPE=\"INS\"' SV_Chr_1.vcf -o SV_Chr_1_INS.vcf<\/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-a792016 elementor-widget elementor-widget-text-editor\" data-id=\"a792016\" 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>\u63d0\u53d6\u540e\u5176\u5b9e\u53ef\u4ee5\u505a\u5f88\u591a\u4e8b\uff0c\u6bd4\u5982\u4f7f\u7528\u5806\u53e0\u67f1\u72b6\u56fe\u5c55\u793a\u6bcf\u6761\u67d3\u8272\u4f53SV\u7684\u6570\u91cf\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-1a5748b elementor-widget elementor-widget-heading\" data-id=\"1a5748b\" 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<h3 class=\"elementor-heading-title elementor-size-default\">3.3 \u7edf\u8ba1SV\u4e2d\u63d2\u5165\u548c\u7f3a\u5931\u7684\u6570\u91cf<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-95e5e73 elementor-widget elementor-widget-code-highlight\" data-id=\"95e5e73\" 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>grep -v '^#' SV_Chr_1_DEL.vcf|wc -l\ngrep -v '^#' SV_Chr_1_INS.vcf|wc -l<\/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-0954442 elementor-widget elementor-widget-heading\" data-id=\"0954442\" 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<h3 class=\"elementor-heading-title elementor-size-default\">3.4 \u7edf\u8ba1\u63d2\u5165\u548c\u7f3a\u5931SV\u7684\u957f\u5ea6<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-574a03f elementor-widget elementor-widget-code-highlight\" data-id=\"574a03f\" 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>bcftools view -i 'abs(SVLEN) < 500' SV_Chr_1_DEL_INS.vcf | grep -v '^#'|wc -l\nbcftools view -i 'abs(SVLEN) > 500 && abs(SVLEN) < 1000' SV_Chr_1_DEL_INS.vcf | grep -v '^#'|wc -l\nbcftools view -i 'abs(SVLEN) > 1000 && abs(SVLEN) < 1500' SV_Chr_1_DEL_INS.vcf | grep -v '^#'|wc -l\nbcftools view -i 'abs(SVLEN) > 1500 && abs(SVLEN) < 2000' SV_Chr_1_DEL_INS.vcf | grep -v '^#'|wc -l\nbcftools view -i 'abs(SVLEN) > 2000 && abs(SVLEN) < 2500' SV_Chr_1_DEL_INS.vcf | grep -v '^#'|wc -l\nbcftools view -i 'abs(SVLEN) > 2500 && abs(SVLEN) < 3000' SV_Chr_1_DEL_INS.vcf | grep -v '^#'|wc -l\nbcftools view -i 'abs(SVLEN) > 3000 && abs(SVLEN) < 3500' SV_Chr_1_DEL_INS.vcf | grep -v '^#'|wc -l\nbcftools view -i 'abs(SVLEN) > 3500 && abs(SVLEN) < 4000' SV_Chr_1_DEL_INS.vcf | grep -v '^#'|wc -l\nbcftools view -i 'abs(SVLEN) > 4000 && abs(SVLEN) < 4500' SV_Chr_1_DEL_INS.vcf | grep -v '^#'|wc -l\nbcftools view -i 'abs(SVLEN) > 4500 && abs(SVLEN) < 5000' SV_Chr_1_DEL_INS.vcf | grep -v '^#'|wc -l\nbcftools view -i 'abs(SVLEN) > 5000' SV_Chr_1_DEL_INS.vcf | grep -v '^#'|wc -l<\/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-6d0bf61 elementor-widget elementor-widget-heading\" data-id=\"6d0bf61\" 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<h3 class=\"elementor-heading-title elementor-size-default\">3.5 \u8ba1\u7b97Pi\u503c<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-8c2b520 elementor-widget elementor-widget-text-editor\" data-id=\"8c2b520\" 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>Vcftools\u8ba1\u7b97Pi\u7684\u65f6\u5019\u5fc5\u987b\u662f\u4e25\u683c\u7684\u4e8c\u500d\u4f53\uff0c\u4e5f\u5c31\u662f\u6709\u4e24\u4e2a\u7b49\u4f4d\u57fa\u56e0\uff0c\u6240\u4ee5\u8981\u5148\u628a\u5355\u500d\u4f53\u4fee\u6539\u4e3a\u4e8c\u500d\u4f53\uff0c\u4e5f\u5c31\u662f\u6dfb\u52a0\u4e00\u4e2a\u7b49\u4f4d\u57fa\u56e0\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-054e61e elementor-widget elementor-widget-code-highlight\" data-id=\"054e61e\" 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>python3 ~\/Script\/Py\/haploids_to_diploids.py SV_Chr_1_DEL_INS.vcf diploids_SV_Chr_1_DEL_INS.vcf\nvcftools --vcf diploids_SV_Chr_1_DEL_INS.vcf --window-pi 1000000 --window-pi-step 200000 --out Test<\/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-2305cdf elementor-widget elementor-widget-heading\" data-id=\"2305cdf\" 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<h3 class=\"elementor-heading-title elementor-size-default\">3.6 \u8ba1\u7b97Fst\u503c<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-3a3461b elementor-widget elementor-widget-code-highlight\" data-id=\"3a3461b\" 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>python3 ~\/Script\/Py\/haploids_to_diploids.py SV_Chr_1_DEL_INS.vcf diploids_SV_Chr_1_DEL_INS.vcf\nvcftools --vcf diploids_SV_Chr_1_DEL_INS.vcf --window-pi 1000000 --window-pi-step 200000 --out Test<\/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-efdf9da elementor-widget elementor-widget-text-editor\" data-id=\"efdf9da\" 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>\u5176\u5b9e\u8fd8\u53ef\u4ee5\u8ba1\u7b97Fst\u6216\u8005\u5176\u4ed6\u8861\u91cf\u79cd\u7fa4\u591a\u6837\u6027\u7684\u6307\u6807\u3002\u4f46\u662fFst\u8ba1\u7b97\u7684\u65f6\u5019\u53ea\u5173\u6ce8\u4e8e\u4e24\u4e2a\u79cd\u7fa4\u4e4b\u95f4\u7684\u6bd4\u8f83\uff0c\u4f46\u662f\u672c\u7814\u7a76\u7684\u7814\u7a76\u5173\u6ce8\u7684\u591a\u4e2a\u79cd\u7fa4\uff0c\u6240\u4ee5\u8fd9\u91cc\u5c31\u4e0d\u5f80\u4e0b\u505a\u4e86\u3002<\/p>\t\t\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 Pggb\u8f93\u51fa\u7684VCF\u6587\u4ef6\u9664\u4e86\u6709SV\u8fd8\u6709SNP\uff0c\u56e0\u6b64\u8981\u628aSV\u5355\u72ec\u63d0\u53d6\u51fa\u6765\uff0c\u540e\u7eed\u6240\u6709\u7684\u5206\u6790\u90fd\u662f\u57fa\u4e8eSV &#8230; <a title=\"VCF\u6587\u4ef6\u4e2d\u7b5b\u9009SV\" class=\"read-more\" href=\"http:\/\/www.majunpeng.com\/index.php\/2025\/06\/11\/vcf%e6%96%87%e4%bb%b6%e4%b8%ad%e7%ad%9b%e9%80%89sv\/\" aria-label=\"\u9605\u8bfb VCF\u6587\u4ef6\u4e2d\u7b5b\u9009SV\">\u9605\u8bfb\u66f4\u591a<\/a><\/p>\n","protected":false},"author":1,"featured_media":1642,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_crdt_document":"","footnotes":""},"categories":[6],"tags":[],"class_list":["post-1641","post","type-post","status-publish","format-standard","has-post-thumbnail","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>VCF\u6587\u4ef6\u4e2d\u7b5b\u9009SV - \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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