{"id":1938,"date":"2025-08-24T21:43:27","date_gmt":"2025-08-24T13:43:27","guid":{"rendered":"http:\/\/www.majunpeng.com\/?p=1938"},"modified":"2026-03-03T23:39:33","modified_gmt":"2026-03-03T15:39:33","slug":"gwas%e5%ad%a6%e4%b9%a0","status":"publish","type":"post","link":"http:\/\/www.majunpeng.com\/index.php\/2025\/08\/24\/gwas%e5%ad%a6%e4%b9%a0\/","title":{"rendered":"GWAS\u5b66\u4e60"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-post\" data-elementor-id=\"1938\" class=\"elementor elementor-1938\" data-elementor-post-type=\"post\">\n\t\t\t\t<div class=\"elementor-element elementor-element-23efe48 e-flex e-con-boxed e-con e-parent\" data-id=\"23efe48\" 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-44f7a96 elementor-widget elementor-widget-heading\" data-id=\"44f7a96\" 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\">0.\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-8407aec elementor-widget elementor-widget-text-editor\" data-id=\"8407aec\" 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>\u4f5c\u4e3a\u4e00\u4e2a\u57fa\u56e0\u7ec4\u5b66\u7814\u7a76\u4eba\u5458\uff0c\u600e\u4e48\u53ef\u4ee5\u4e0d\u4f1aGWAS\u5462\uff1f\u6700\u8fd1\u63a5\u4e86\u4e00\u4e2aGWAS\u7684\u9879\u76ee\uff0c\u6b63\u597d\u501f\u7740\u8fd9\u4e2a\u673a\u4f1a\u8fb9\u505a\u8fb9\u5b66GWAS\u3002\uff08\u52a0\u7b14\uff1a\u8017\u65f6\u534a\u4e2a\u6708\uff0c\u5927\u81f4\u5b66\u5b8c\u4e86GWAS\u7684\u6d41\u7a0b\uff0c\u6709\u4e00\u4e2a\u521d\u6b65\u7684\u7406\u89e3\u3002\u867d\u7136GWAS\u662f\u65e9\u5c31\u51fa\u73b0\u7684\u6280\u672f\uff0c\u4f46\u662f\u653e\u5230\u4eca\u5929\u786e\u5b9e\u4e0d\u8fc7\u65f6\uff0c\u901a\u8fc7\u5c06SNP\u7b49\u53d8\u5f02\u548c\u8868\u578b\u6570\u636e\u5173\u8054\uff0c\u5f97\u5230\u76f8\u5173\u7684\u4f4d\u70b9\uff0c\u786e\u5b9e\u80fd\u6bd4\u8f83\u7cbe\u51c6\u7684\u5f97\u5230\u548c\u5173\u952e\u6027\u72b6\u76f8\u5173\u7684\u57fa\u56e0\u3002\u4f46\u662f\uff01\u5982\u679c\u60f3\u5f97\u5230\u51c6\u786e\u7684\u7ed3\u679c\uff0c\u5206\u6790\u7684\u6d41\u7a0b\u8981\u975e\u5e38\u6807\u51c6\uff0c\u6bd4\u5982\u8868\u578b\u7684\u91c7\u96c6\u548c\u8bb0\u5f55\uff0c\u5927\u591a\u4eba\u4f1a\u4f4e\u4f30\u8fd9\u4e00\u6b65\uff0c\u4f46\u662f\u6211\u8ba4\u4e3a\u662f\u6bd4\u8f83\u91cd\u8981\u7684\u3002\u5982\u679c\u9519\u8bef\u7684\u8868\u578b\u5f88\u6709\u53ef\u80fd\u4f1a\u5bfc\u81f4\u4e0d\u80fd\u627e\u5230\u51c6\u786e\u7684SNP\u4f4d\u70b9\uff0c\u6216\u8005\u6839\u672c\u627e\u4e0d\u5230SNP\u4f4d\u70b9\uff0c\u5206\u6790\u51fa\u82b1\u6765\u90fd\u6ca1\u7528\u3002\u53e6\u5916GWAS\u5206\u6790\u7684\u4e3b\u6d41\u8f6f\u4ef6\u548c\u6a21\u578b\u56de\u5bf9\u7ed3\u679c\u6709\u8f83\u660e\u663e\u7684\u7ed3\u679c\uff0c\u6240\u4ee5\u5982\u679c\u7ed3\u679c\u4e0d\u597d\uff0c\u6216\u8005\u627e\u4e0d\u5230P\u503c\u660e\u663e\u7684\u70b9\uff0c\u53ef\u4ee5\u6362\u6a21\u578b\u8bd5\u4e00\u4e0b\u3002\u6700\u540e\uff0c\u521d\u5b66\u8005\u53ef\u80fd\u89c9\u5f97\u627e\u5230SNP\u4f4d\u70b9\u5c31\u7ed3\u675f\u4e86\uff0c\u4f46\u662f\u5f88\u6709\u53ef\u80fdSNP\u4f4d\u70b9\u538b\u6839\u4e0d\u5728\u57fa\u56e0\u4e2d\uff0c\u8fd9\u65f6\u5019\u5c31\u9700\u8981\u901a\u8fc7\u5176\u4ed6\u8f6f\u4ef6\u6765\u8ba1\u7b97\u8fde\u9501\u4e0d\u5e73\u8861\uff0c\u6765\u627e\u5230\u548cSNP\u4f4d\u70b9\u5177\u6709\u4e0d\u5e73\u8861\u7684\u57fa\u56e0\uff0c\u4f5c\u4e3a\u5019\u9009\u57fa\u56e0\u3002\uff09<\/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-a340c22 elementor-widget elementor-widget-text-editor\" data-id=\"a340c22\" 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>\u6b63\u5f0f\u5f00\u59cb\u4e4b\u524d\uff0c\u5148\u653e\u4e00\u4e9b\u548cVCF\u6587\u4ef6\u5904\u7406\u548c\u8fc7\u6ee4\u76f8\u5173\u7684\u547d\u4ee4\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-f3c3332 elementor-widget elementor-widget-heading\" data-id=\"f3c3332\" 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\">0.1 \u7edf\u8ba1\u5e76\u53ef\u89c6\u5316VCF\u6587\u4ef6\u4e2dSNP\u4f4d\u70b9\u7684\u7f3a\u5931\u7387<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-c914a09 elementor-widget elementor-widget-code-highlight\" data-id=\"c914a09\" 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># Stat\nplink --vcf Rename_snps.f4.withid.75samples.RNAseqID.vcf --missing --out demo\n# Plot\n<\/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-5bc7f2a elementor-widget elementor-widget-heading\" data-id=\"5bc7f2a\" 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\">0.2 \u5bf9\u57fa\u56e0\u578b\u4f4d\u70b9\u8fdb\u884c\u8fc7\u6ee4<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-d849670 elementor-widget elementor-widget-code-highlight\" data-id=\"d849670\" 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>plink --vcf  demo.vcf --out demo.final_clean  --recode vcf-iid  --remove  demo.fail.samples  --make-bed --geno 0.1 --maf 0.05  --biallelic-only strict  --hwe 1e-6  -set-missing-var-ids @:#  --allow-extra-chr<\/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-b4a719d elementor-widget elementor-widget-heading\" data-id=\"b4a719d\" 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\">0.3 \u5bf9\u57fa\u56e0\u578b\u4f4d\u70b9\u8fdb\u884c\u586b\u5145<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-8c59db9 elementor-widget elementor-widget-code-highlight\" data-id=\"8c59db9\" 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>beagle -Xmx4g -Djava.io.tmpdir=.\/TMP  gt=.\/demo.final_clean.vcf out=demo.impute impute=true  window=10 nthreads=4<\/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-caa6ddd elementor-widget elementor-widget-heading\" data-id=\"caa6ddd\" 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\">0.4 \u68c0\u67e5\u8868\u578b\u6570\u636e\u7684\u6b63\u6001\u6027<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-58efa63 elementor-widget elementor-widget-code-highlight\" data-id=\"58efa63\" 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>Rscript  ..\/script\/phenotype_check.R   ..\/data\/demo_traits.txt   traits_check<\/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-437486f elementor-widget elementor-widget-heading\" data-id=\"437486f\" 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\">0.4 \u8ba1\u7b97\u4eb2\u7f18\u5173\u7cfb\u77e9\u9635<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-ba94cba elementor-widget elementor-widget-code-highlight\" data-id=\"ba94cba\" 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>gcta --bfile ..\/00.prepare\/demo   --make-grm-gz  --make-grm-alg 0  --out  gcta_kinship\n\n## \u66ff\u6362sample name ; \u8f6c\u6210\u5bf9\u89d2\u77e9\u9635\ngzip -d gcta_kinship.grm.gz\n\nawk -v OFS=\"\\t\" 'NR==FNR{ A[ NR ] = $1}; NR>FNR{ if( $1 in A && $2 in A){ $1 = A[$1]; $2 = A[$2] ; print $0}}'  gcta_kinship.grm.id gcta_kinship.grm  > gcta_kinship.grm.addname.pairwise\n\nawk -v OFS=\"\\t\" '{if(NR==FNR){ A[NR] = $1; max=NR } else { B[$1][$2] = $4; B[$2][$1] = $4 } } END { for( i=1; i<=max; i++){ printf A[i] ; for(j=1; j<=max; j++){printf \"\\t\"B[i][j]} ; print \"\" }}'  gcta_kinship.grm.id gcta_kinship.grm  > gcta_kinship.grm.addname.matrix<\/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-0235c31 elementor-widget elementor-widget-heading\" data-id=\"0235c31\" 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. \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-93d3057 elementor-widget elementor-widget-code-highlight\" data-id=\"93d3057\" 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 GWAS\nmamba activate GWAS\n# plink\nconda install bioconda::plink\n# emmax\nwget https:\/\/csg.sph.umich.edu\/\/kang\/emmax\/download\/emmax-intel-binary-20120210.tar.gz\ntar xvf emmax-intel-binary-20120210.tar.gz\n# tassel\nmamba install bioconda::tassel\n# rMVP\ninstall.packages(\"rMVP\")\n# GAPIT\nhttps:\/\/github.com\/jiabowang\/GAPIT\n\n<\/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-6ed872e elementor-widget elementor-widget-heading\" data-id=\"6ed872e\" 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. \u683c\u5f0f\u8f6c\u5316<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-bb1c31e elementor-widget elementor-widget-text-editor\" data-id=\"bb1c31e\" 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>\u8868\u73b0\u6570\u636e\u683c\u5f0f\u5982\u4e0b<\/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-19405e3 elementor-widget elementor-widget-code-highlight\" data-id=\"19405e3\" 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>RNAseq_ID        GD10Y \nX07      45.21 \nX08      36.63 \nX02      30.25 \nX09      35.16 \nX06      43.14 \nX10      36.30 \nX11      41.05 \nX12      34.07 \nX13      48.23<\/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-f22d149 elementor-widget elementor-widget-text-editor\" data-id=\"f22d149\" 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>emmax\u8981\u6c42\u8f93\u5165\u7684\u6570\u636e\u4e0d\u80fd\u662fvcf\u683c\u5f0f\uff0c\u56e0\u6b64\u5148\u4f7f\u7528plink\u8fdb\u884c\u683c\u5f0f\u8f6c\u6362\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-f0f87cf elementor-widget elementor-widget-code-highlight\" data-id=\"f0f87cf\" 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>plink --vcf snps.f4.withid.75samples.RNAseqID.vcf --maf 0.05 --geno 0.1 --recode 12 transpose  --output-missing-genotype 0  --out snp_filter   --set-missing-var-ids @:#  --allow-extra-chr  --keep-allele-order\n\n  --vcf snps.f4.withid.75samples.RNAseqID.vcf: \u6307\u5b9a\u8f93\u5165\u7684 VCF \u6587\u4ef6\u540d\u3002VCF (Variant Call Format) \u662f\u5b58\u50a8\u57fa\u56e0\u53d8\u5f02\u4fe1\u606f\u7684\u6807\u51c6\u683c\u5f0f\u3002\n  --maf 0.05: \u6309\u6b21\u8981\u7b49\u4f4d\u57fa\u56e0\u9891\u7387\uff08Minor Allele Frequency, MAF\uff09\u8fdb\u884c\u8fc7\u6ee4\u3002\u6b64\u53c2\u6570\u4f1a\u79fb\u9664\u6570\u636e\u96c6\u4e2d MAF \u4f4e\u4e8e 5% \u7684\u6240\u6709 SNP\uff08\u5355\u6838\u82f7\u9178\u591a\u6001\u6027\uff09\u3002\n  --geno 0.1: \u6309\u57fa\u56e0\u578b\u7f3a\u5931\u7387\u8fdb\u884c\u8fc7\u6ee4\u3002\u6b64\u53c2\u6570\u4f1a\u79fb\u9664\u5728\u8d85\u8fc7 10% \u7684\u6837\u672c\u4e2d\u672a\u80fd\u6210\u529f\u8fdb\u884c\u57fa\u56e0\u5206\u578b\u7684 SNP\u3002\n  --recode 12 transpose: \u6307\u5b9a\u8f93\u51fa\u6587\u4ef6\u7684\u683c\u5f0f\u3002\n  'recode 12': \u5c06\u57fa\u56e0\u578b\u6570\u636e\u91cd\u65b0\u7f16\u7801\u4e3a\u6570\u5b57\uff1a0 \u4ee3\u8868\u7eaf\u5408\u53c2\u8003\u57fa\u56e0\u578b\uff08\u5982 A\/A\uff09\uff0c1 \u4ee3\u8868\u6742\u5408\u57fa\u56e0\u578b\uff08\u5982 A\/G\uff09\uff0c2 \u4ee3\u8868\u7eaf\u5408\u5907\u9009\u57fa\u56e0\u578b\uff08\u5982 G\/G\uff09\u3002\n  'transpose': \u5c06\u8f93\u51fa\u7684\u77e9\u9635\u8f6c\u7f6e\uff0c\u4f7f\u5f97\u884c\u4e3a\u6837\u672c\uff08Sample\uff09\uff0c\u5217\u4e3a SNP\u3002\u8fd9\u5728\u5f88\u591a\u7edf\u8ba1\u5206\u6790\uff08\u5982 R \u8bed\u8a00\uff09\u4e2d\u662f\u5e38\u89c1\u7684\u8f93\u5165\u683c\u5f0f\u3002\n  --output-missing-genotype 0: \u6307\u5b9a\u5728\u8f93\u51fa\u6587\u4ef6\u4e2d\u5982\u4f55\u8868\u793a\u7f3a\u5931\u7684\u57fa\u56e0\u578b\u3002\u8fd9\u91cc\u7528 '0' \u6765\u4ee3\u66ff\u7f3a\u5931\u503c\u3002\u6ce8\u610f\uff1a\u8fd9\u53ef\u80fd\u4f1a\u4e0e\u4ee3\u8868\u7eaf\u5408\u53c2\u8003\u57fa\u56e0\u578b\u7684 '0' \u4ea7\u751f\u6df7\u6dc6\uff0c\u5728\u540e\u7eed\u5206\u6790\u4e2d\u9700\u8981\u7279\u522b\u7559\u610f\u3002\n  --out snp_filter: \u6307\u5b9a\u8f93\u51fa\u6587\u4ef6\u7684\u524d\u7f00\u3002\u6240\u6709\u751f\u6210\u7684\u6587\u4ef6\u90fd\u5c06\u4ee5 \"snp_filter\" \u5f00\u5934\uff0c\u4f8b\u5982 snp_filter.ped\u3002\n  --set-missing-var-ids @:#: \u4e3a\u90a3\u4e9b\u5728 VCF \u6587\u4ef6\u4e2d\u6ca1\u6709 ID\uff08\u901a\u5e38\u8868\u793a\u4e3a \".\"\uff09\u7684\u53d8\u5f02\u4f4d\u70b9\u521b\u5efa\u4e00\u4e2a\u65b0\u7684 ID\u3002\u8fd9\u4e2a\u6a21\u677f\u4f1a\u4f7f\u7528\u67d3\u8272\u4f53\u540d\uff08\u7531@\u4ee3\u8868\uff09\u548c\u7269\u7406\u4f4d\u7f6e\uff08\u7531#\u4ee3\u8868\uff09\u6765\u751f\u6210 ID\uff0c\u683c\u5f0f\u5982 chr1:12345\u3002\n  --allow-extra-chr: \u5141\u8bb8 VCF \u6587\u4ef6\u4e2d\u5305\u542b\u975e\u6807\u51c6\u6216\u975e\u5e38\u89c4\u7684\u67d3\u8272\u4f53\u540d\u79f0\uff08\u4f8b\u5982\uff0cscaffolds \u6216 contigs\uff09\uff0c\u8fd9\u5728\u5904\u7406\u975e\u6a21\u5f0f\u751f\u7269\u7684\u57fa\u56e0\u7ec4\u6570\u636e\u65f6\u975e\u5e38\u6709\u7528\u3002\n  --keep-allele-order: \u5f3a\u5236 PLINK \u4fdd\u6301 VCF \u6587\u4ef6\u4e2d\u5b9a\u4e49\u7684\u53c2\u8003\u7b49\u4f4d\u57fa\u56e0\uff08REF\uff09\u548c\u5907\u9009\u7b49\u4f4d\u57fa\u56e0\uff08ALT\uff09\u7684\u987a\u5e8f\u3002\u9ed8\u8ba4\u60c5\u51b5\u4e0b\uff0cPLINK \u53ef\u80fd\u4f1a\u4e3a\u4e86\u65b9\u4fbf\u5185\u90e8\u5904\u7406\u800c\u4ea4\u6362\u5b83\u4eec\u3002\n  \n  #snp_filter.log\uff0csnp_filter.nosex\uff0csnp_filter.tfam\uff0csnp_filter.tped\u3002\u8fd9\u56db\u4e2a\u6587\u4ef6\u662f\u8f93\u51fa\u6587\u4ef6\uff0c\u540e\u9762\u4f1a\u7528\u5230\u3002<\/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-1f887bc elementor-widget elementor-widget-text-editor\" data-id=\"1f887bc\" 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>emmax\u8981\u6c42\u6027\u72b6\u7279\u5f81\u7684\u6587\u672c\u6587\u4ef6\u7684\u987a\u5e8f\u8981\u548cVCF\u6587\u4ef6\u7684\u4e00\u81f4\uff0c\u8fd9\u91cc\u7528\u4e00\u4e2a\u811a\u672c\u6765\u8fdb\u884c\u6392\u5e8f\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-8b4ba89 elementor-widget elementor-widget-code-highlight\" data-id=\"8b4ba89\" 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 ort_pheno.pl snp_filter.tfam GD10_Triat.txt > Sort_GD10_Triat.txt<\/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-a02b569 elementor-widget elementor-widget-text-editor\" data-id=\"a02b569\" 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>\u8fd8\u8981\u751f\u6210\u4eb2\u7f18\u5173\u7cfb\u77e9\u9635\uff0cgwas\u5206\u6790\u7684\u65f6\u5019\u4f5c\u4e3a\u77eb\u6b63<\/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-72759c6 elementor-widget elementor-widget-code-highlight\" data-id=\"72759c6\" 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>~\/Software\/emmax\/emmax-kin-intel64 -v -d 10  -o .\/pop.kinship  snp_filter\n\n# snp_filter \u8f93\u5165\u8f93\u5165\u6587\u4ef6\u7684\u524d\u7f00\n# -o \u7ed3\u679c\u6587\u4ef6<\/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-12d344c elementor-widget elementor-widget-heading\" data-id=\"12d344c\" 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. GWAS\u5206\u6790<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-1f2fb31 elementor-widget elementor-widget-text-editor\" data-id=\"1f2fb31\" 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>\u5206\u6790\u4e4b\u524d\u8981\u5f3a\u8c03\u4ee5\u4e0b\uff0c\u4e0d\u540c\u7684\u8f6f\u4ef6\u652f\u6301\u4e0d\u540c\u7684\u6a21\u578b\uff0c\u5e76\u4e14\u5728\u5206\u6790\u7684\u65f6\u5019\u53ef\u80fd\u4f1a\u52a0\u5165\u4eb2\u7f18\u5173\u7cfb\u77e9\u9635\uff0cPCA\u77e9\u9635\u6216\u8005Q\u77e9\u9635\u4f5c\u4e3a\u7fa4\u4f53\u7ed3\u6784\u77eb\u6b63\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-1cb13b5 elementor-widget elementor-widget-shortcode\" data-id=\"1cb13b5\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"shortcode.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-shortcode\">\n<table id=\"tablepress-16\" class=\"tablepress tablepress-id-16\">\n<thead>\n<tr class=\"row-1 odd\">\n\t<th class=\"column-1\">\u8f6f\u4ef6<\/th><th class=\"column-2\">\u8fd0\u7b97\u901f\u5ea6<\/th><th class=\"column-3\">\u6a21\u578b\u6570\u91cf<\/th><th class=\"column-4\">\u7ed3\u679c\u5c55\u793a<\/th>\n<\/tr>\n<\/thead>\n<tbody class=\"row-hover\">\n<tr class=\"row-2 even\">\n\t<td class=\"column-1\">EMMAX<\/td><td class=\"column-2\">\u901f\u5ea6\u8f83\u5feb\uff0c\u9002\u7528\u4e8e\u5927\u89c4\u6a21\u6570\u636e<\/td><td class=\"column-3\">MLM<\/td><td class=\"column-4\">\u8f93\u51fa\u7b80\u5355\uff0c\u4ec5\u6709\u6587\u672c\u4fe1\u606f<\/td>\n<\/tr>\n<tr class=\"row-3 odd\">\n\t<td class=\"column-1\">TASSEL<\/td><td class=\"column-2\">\u5bf9\u5927\u6570\u636e\u96c6\u5904\u7406\u8f83\u6162<\/td><td class=\"column-3\">GLM\u3001MLM\u3001CMLM<\/td><td class=\"column-4\">\u8f93\u51fa\u7b80\u5355\uff0c\u4ec5\u6709\u6587\u672c\u4fe1\u606f<\/td>\n<\/tr>\n<tr class=\"row-4 even\">\n\t<td class=\"column-1\">GAPIT<\/td><td class=\"column-2\">\u8f83\u6162\uff0c\u9002\u7528\u4e8e\u4e2d\u7b49\u89c4\u6a21\u6570\u636e<\/td><td class=\"column-3\">GLM\u3001FarmCPU\u3001MLM\u3001GLM\u3001CMLM\u3001MMLM\u3001SUPER<\/td><td class=\"column-4\">\u66fc\u54c8\u987f\u56fe\u548cQQplot\u56fe<\/td>\n<\/tr>\n<tr class=\"row-5 odd\">\n\t<td class=\"column-1\">rMVP<\/td><td class=\"column-2\">\u901f\u5ea6\u8f83\u5feb\uff0c\u652f\u6301\u5927\u6570\u636e\u5e76\u884c\u8ba1\u7b97<\/td><td class=\"column-3\">GLM\u3001MLM\u3001FarmCPU<\/td><td class=\"column-4\">\u66fc\u54c8\u987f\u56fe\u548cQQplot\u56fe<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<!-- #tablepress-16 from cache --><\/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-2717fb6 elementor-widget elementor-widget-heading\" data-id=\"2717fb6\" 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 emmax<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-3a1b594 elementor-widget elementor-widget-text-editor\" data-id=\"3a1b594\" 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>emmax\u53ea\u9700\u8981\u8f93\u5165\u4eb2\u7f18\u5173\u7cfb\u77e9\u9635\u5373\u53ef\uff0c\u8f6f\u4ef6\u4f1a\u81ea\u52a8\u8ba1\u7b97\u7fa4\u4f53\u7ed3\u6784\uff0c\u4e0d\u5982\u8981\u989d\u5916\u7684PCA\u6216Q\u77e9\u9635\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-be3f67d elementor-widget elementor-widget-code-highlight\" data-id=\"be3f67d\" 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>~\/Software\/emmax\/emmax-intel64 -v -d 10 -t snp_filter -p Sort_GD10_Triat.txt -k pop.kinship -o emmax.out\n\n  -v: \u542f\u7528\u8be6\u7ec6\u8f93\u51fa\u6a21\u5f0f\uff08verbose\uff09\u3002\u7a0b\u5e8f\u5728\u8fd0\u884c\u65f6\u4f1a\u6253\u5370\u66f4\u8be6\u7ec6\u7684\u8fdb\u5ea6\u548c\u8bca\u65ad\u4fe1\u606f\uff0c\u4fbf\u4e8e\u76d1\u63a7\u548c\u8c03\u8bd5\u3002\n  -d 10: \u8bbe\u7f6e\u8c03\u8bd5\u4fe1\u606f\u7684\u8f93\u51fa\u9891\u7387\u3002\u5177\u4f53\u6765\u8bf4\uff0c\u7a0b\u5e8f\u6bcf\u5904\u7406 10 \u4e2a\u6807\u8bb0\uff08markers\/SNPs\uff09\u5c31\u4f1a\u8f93\u51fa\u4e00\u6b21\u8c03\u8bd5\u4fe1\u606f\uff0c\u65b9\u4fbf\u8ddf\u8e2a\u5206\u6790\u8fdb\u5ea6\u3002\n  -t snp_filter: \u6307\u5b9a\u57fa\u56e0\u578b\u6587\u4ef6\u7684\u57fa\u672c\u540d\u79f0\uff08basename\uff09\u3002EMMAX \u901a\u5e38\u9700\u8981 `.tped` \u548c `.tfam` \u683c\u5f0f\u7684\u6587\u4ef6\u3002\u6b64\u53c2\u6570\u544a\u8bc9\u7a0b\u5e8f\u67e5\u627e\u540d\u4e3a `snp_filter.tped\uff08\u5305\u542b\u57fa\u56e0\u578b\u6570\u636e\uff09\u548c \n  snp_filter.tfam`\uff08\u5305\u542b\u5bb6\u7cfb\u6216\u4e2a\u4f53\u4fe1\u606f\uff09\u7684\u6587\u4ef6\u3002\n  -p Sort_GD10_Triat.txt: \u6307\u5b9a\u8868\u578b\u6570\u636e\u6587\u4ef6\u3002Sort_GD10_Triat.txt \u6587\u4ef6\u5305\u542b\u4e86\u5206\u6790\u4e2d\u6bcf\u4e2a\u4e2a\u4f53\u7684\u8868\u578b\u503c\u3002\u6587\u4ef6\u4e2d\u7684\u4e2a\u4f53\u5fc5\u987b\u4e0e\u57fa\u56e0\u578b\u6587\u4ef6\uff08.tfam\uff09\u4e2d\u7684\u4e2a\u4f53\u76f8\u5bf9\u5e94\u3002\n  -k pop.kinship: \u6307\u5b9a\u4eb2\u7f18\u5173\u7cfb\u77e9\u9635\u6587\u4ef6\u3002pop.kinship \u6587\u4ef6\u662f\u4e00\u4e2a\u65b9\u5dee-\u534f\u65b9\u5dee\u77e9\u9635\uff0c\u7528\u4e8e\u6a21\u62df\u4e2a\u4f53\u95f4\u7684\u9057\u4f20\u76f8\u5173\u6027\u3002\u8fd9\u662f EMMAX \n  \u6df7\u5408\u6a21\u578b\u65b9\u6cd5\u7684\u6838\u5fc3\uff0c\u901a\u8fc7\u5b83\u6765\u6821\u6b63\u7fa4\u4f53\u5206\u5c42\u548c\u9690\u6027\u4eb2\u7f18\u5173\u7cfb\uff0c\u4ece\u800c\u51cf\u5c11\u5047\u9633\u6027\u7ed3\u679c\u3002\n  -o emmax.out: \u6307\u5b9a\u8f93\u51fa\u6587\u4ef6\u7684\u524d\u7f00\u3002\u5206\u6790\u7ed3\u679c\u5c06\u4fdd\u5b58\u5728\u4ee5 emmax.out \u5f00\u5934\u7684\u591a\u4e2a\u6587\u4ef6\u4e2d\u3002\u5176\u4e2d\uff0c\u6700\u4e3b\u8981\u7684\u7ed3\u679c\u6587\u4ef6\u901a\u5e38\u662f emmax.out.ps\uff0c\u5305\u542b\u4e86\u6bcf\u4e2a SNP \u7684\u5173\u8054\u5206\u6790 p \u503c\u7b49\u4fe1\u606f\u3002<\/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-4cfb275 elementor-widget elementor-widget-text-editor\" data-id=\"4cfb275\" 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>\u8fd8\u9700\u8981\u5bf9\u539f\u59cb\u7684GWAS\u7ed3\u679c\u8fdb\u884c\u683c\u5f0f\u8f6c\u6362\uff0c\u65b9\u4fbf\u540e\u7eed\u7ed8\u5236\u66fc\u54c8\u987f\u548cqq\u56fe\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-7f10f0f elementor-widget elementor-widget-code-highlight\" data-id=\"7f10f0f\" 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>awk  '{print $1\"\\t\"$2\"\\t\"$3\"\\t\"$4\"\\t\"}' snp_filter.tped |paste - emmax.out.ps |  awk  'BEGIN{print \"SNP\\tCHR\\tBP\\tP\"}{if($2==$5){print $2\"\\t\"$1\"\\t\"$4\"\\t\"$NF}}'  > emmax.out.ps.manht_input<\/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-1ded7bd elementor-widget elementor-widget-heading\" data-id=\"1ded7bd\" 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 tassle<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-06987d7 elementor-widget elementor-widget-text-editor\" data-id=\"06987d7\" 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>tassle\u53ef\u4ee5\u6307\u5b9a\u7fa4\u4f53\u7ed3\u6784\u6587\u4ef6\uff0c\u5373PCA\u6216\u8005Q\u77e9\u9635\uff0c\u4eb2\u7f18\u5173\u7cfb\u77e9\u9635\u4e0d\u9700\u8981\u3002\u53ef\u4ee5\u4f7f\u7528gml,mlm\u548ccmlm\u6a21\u578bGWAS\u5206\u6790\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-663c342 elementor-widget elementor-widget-code-highlight\" data-id=\"663c342\" 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># Triat_format\nhead ..\/GD10_Triat.txt \n\n<Trait> C16_0\nRNAseq_ID        GD10Y \nX07      45.21 \nX08      36.63 \nX02      30.25 \nX09      35.16 \nX06      43.14 \nX10      36.30 \nX11      41.05 \nX12      34.07\n\n# \u4f7f\u7528Q\u9700\u8981\u53bb\u9664\u6700\u540e\u4e00\u5217\nawk '{print $1}' ..\/data\/demo.nosex | paste - ..\/data\/demo.3.Q |awk 'NR==1{printf \"<Covariate>\\n<Trait>\";for(i=1; i<NF-1; i++){printf \"\\tQ\"i}; printf \"\\n\"}; {NF--; print $0}' >  Qdata.txt\n\n# Q format\nhead ..\/Qdata.txt     \n<Covariate>\n<Trait> Q1      Q2\nX01 0.078568 0.844972\nX02 0.999980 0.000010\nX03 0.714090 0.285900\nX04 0.975353 0.000010\nX05 0.000010 0.999980\nX06 0.999980 0.000010\nX07 0.000010 0.866252\nX08 0.083799 0.860377\n\n# \u4e5f\u53ef\u4f7f\u7528\u524d3\u4e2a\u4e3b\u6210\u5206\nsed 's\/\\s\\+\/\\t\/g' ..\/data\/demo.PCA.eigenvec| cut -f 2-5 |awk 'NR==1{printf \"<Covariate>\\n<Trait>\";for(i=1; i<NF; i++){printf \"\\tP\"i}; printf \"\\n\"}; {print $0}' >  Qdata.txt\n\n## \u8ba1\u7b97\u4eb2\u7f18\u5173\u7cfb\nrun_pipeline.pl -Xms512m -Xmx10g -importGuess demo.sort.vcf  -KinshipPlugin -method Centered_IBS -endPlugin -export kinship.txt -exportType SqrMatrix\n\n# Run GWAS with gml model\nrun_pipeline.pl -Xms512m -Xmx10g \\\n  -fork1 -vcf demo.sort.vcf   \\\n  -fork2  -t trait.txt \\\n  -fork3 -q  Qdata.txt  \\\n  -combine4 -input1 -input2 -input3 -intersect \\\n  -FixedEffectLMPlugin -endPlugin \\\n  -export glm_output\n \n# Run GWAS with mlm model\nrun_pipeline.pl -Xms512m -Xmx20g \\\n  -fork1 -vcf demo.sort.vcf \\\n  -fork2 -t   trait.txt \\\n  -fork3 -q   Qdata.txt \\\n  -fork4 -k   kinship.txt  \\\n  -combine5 -input1 -input2 -input3 -intersect \\\n  -combine6 -input5 -input4 -mlm \\\n  -mlmVarCompEst P3D -mlmCompressionLevel  None\\\n  -export mlm_output\n  \n# Run GWAS with cmlm model\nrun_pipeline.pl -Xms512m -Xmx20g \\\n  -fork1 -vcf demo.sort.vcf  \\\n  -fork2 -t  trait.txt \\\n  -fork3 -q  Qdata.txt \\\n  -fork4 -k  kinship.txt  \\\n  -combine5 -input1 -input2 -input3 -intersect \\\n  -combine6 -input5 -input4 -mlm \\\n  -mlmVarCompEst P3D -mlmCompressionLevel Optimum \\\n  -export cmlm_output\n\n# \u8c03\u6574\u683c\u5f0f\uff0c\u65b9\u4fbf\u7ed8\u56fe\nawk '{print $2\"\\t\"$3\"\\t\"$4\"\\t\"$7}' cmlm_output2.txt  | awk '$NF ~ \/[0-9]+\/ || NR == 1 ' > cmlm_output.manht_input<\/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-94a5e1b elementor-widget elementor-widget-heading\" data-id=\"94a5e1b\" 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 GAPIT<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-d2cc204 elementor-widget elementor-widget-text-editor\" data-id=\"d2cc204\" 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>GPAIT\u7ed9\u6211\u7684\u7b2c\u4e00\u5370\u8c61\u5c31\u662f\u4e00\u4e2a\u5b57\u201c\u5168\u201d\uff0c\u662f\u6240\u6709GWAS\u5206\u6790\u4e2d\u652f\u6301\u7684\u6a21\u578b\u6700\u591a\u7684\uff0c\u7f3a\u70b9\u5c31\u662f\u901f\u5ea6\u8f83\u6162\u3002\u5e76\u4e14\u4e0d\u9700\u8981\u8981\u8f93\u5165\u4eb2\u7f18\u5173\u7cfb\u77e9\u9635\u548c\u7fa4\u4f53\u7ed3\u6784\u6587\u4ef6\uff0c\u8f6f\u4ef6\u4f1a\u81ea\u52a8\u8ba1\u7b97\u5e76\u8fdb\u884c\u77eb\u6b63\u3002\u8f93\u5165\u7684\u57fa\u56e0\u578b\u6570\u636e\u8981\u6c42\u662fhmp\u683c\u5f0f\u7684\u3002\u6b64\u5916\uff0c\u8be5\u8f6f\u4ef6\u662f\u4e2aR\u5305\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-9581dfa elementor-widget elementor-widget-code-highlight\" data-id=\"9581dfa\" 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># Trait dir format\nhead trait.txt\n\nTaxa    GD10    GD5     ZG\nX01     35.22   39.1    197.0\nX02     30.25   32.53   224.0\nX03     39.27   49.52   274.3\nX04     NA      57.6    265.5\nX05     40.95   42.8    185.0\nX06     43.14   45.74   238.5\nX07     45.21   46.22   184.5\nX08     36.63   37.66   188.5\nX09     35.16   36.08   203.0\n\n## \u51c6\u5907\u57fa\u56e0\u578b\u6570\u636e\nrun_pipeline.pl -Xms1G -Xmx5G   -importGuess  ..\/data\/demo.vcf  -ExportPlugin -format  HapmapDiploid -saveAs demo.hmp.txt\nsed -i '1s\/#\/\/g'  demo.hmp.txt<\/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-73d829e elementor-widget elementor-widget-text-editor\" data-id=\"73d829e\" 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>\u8fd0\u884cGAPIT\u7684R\u811a\u672c<\/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-f00e5e7 elementor-widget elementor-widget-heading\" data-id=\"f00e5e7\" 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 rMVP<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-b356bd7 elementor-widget elementor-widget-text-editor\" data-id=\"b356bd7\" 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>\u540c\u6837\u662f\u4e00\u4e2a\u505aGWAS\u5206\u6790\u7684R\u811a\u672c\uff0c\u76f8\u6bd4\u4e8eGAPIT\uff0c\u6a21\u578b\u8f83\u5c11\uff0c\u4f46\u662f\u901f\u5ea6\u5feb\uff0c\u51fa\u56fe\u597d\u770b\uff0c\u76f4\u63a5\u5c31\u53ef\u4ee5\u8f93\u5165VCF\u6587\u4ef6\u3002\u540c\u6837\u4e0d\u521a\u9700\u4eb2\u7f18\u5173\u7cfb\u77e9\u9635\u548c\u7fa4\u4f53\u7ed3\u6784\u6587\u4ef6\uff0c\u8f6f\u4ef6\u4f1a\u81ea\u52a8\u7ed3\u7b97\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-6618b94 elementor-widget elementor-widget-code-highlight\" data-id=\"6618b94\" 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># Trait dir format\nhead trait.txt\n\nTaxa    GD10    GD5     ZG\nX01     35.22   39.1    197.0\nX02     30.25   32.53   224.0\nX03     39.27   49.52   274.3\nX04     NA      57.6    265.5\nX05     40.95   42.8    185.0\nX06     43.14   45.74   238.5\nX07     45.21   46.22   184.5\nX08     36.63   37.66   188.5\nX09     35.16   36.08   203.0<\/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-ed19101 elementor-widget elementor-widget-text-editor\" data-id=\"ed19101\" 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>\u8fd0\u884crMVP\u7684R\u811a\u672c<\/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-d35b2b3 elementor-widget elementor-widget-code-highlight\" data-id=\"d35b2b3\" 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-r line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-r\">\n\t\t\t\t\t<xmp># Run GWAS with rMVP\nlibrary(rMVP)\n# genotype\u6570\u636e\u5b58\u50a8\u4e3aMVP\u683c\u5f0f\nMVP.Data(fileVCF=\".\/demo.vcf\",\n         #fileHMP=\"hapmap.txt\",\n         #fileBed=\"plink\",\n         filePhe=\"trait.txt\",\n         fileKin=F,\n         filePC=F,\n         out=\"mvp\",\n         ncpus = 5\n)\n\n# \u8bfb\u53d6genotyp\u548c\u8868\u578b\u6570\u636e\ngenotype <- attach.big.matrix(\"mvp.geno.desc\")\nmap <- read.table(\"mvp.geno.map\" , head = TRUE)\nphenotype <- read.table(\"mvp.phe\",head=TRUE)\n\n## \u53ef\u5355\u72ec\u8ba1\u7b97Kinship\u548cPC\nK <- MVP.K.VanRaden(genotype)\nPC <- MVP.PCA(genotype,pcs.keep = 5)\nwrite.table(K, file = \"kinship.matrix\", sep=\"\\t\",quote = F, row.names = F, col.names = \nF)\nwrite.table(PC, file = \"PC.matrix\", sep=\"\\t\",quote = F, row.names = F, col.names = F)\n\n\n# \u652f\u6301\u6a21\u578b GLM, MLM \u548c FarmCPU.\nimMVP <- MVP(\n  phe=phenotype,\n  geno=genotype,\n  map=map,\n  #K=Kinship,\n  #CV.GLM=Covariates,  ##if you have additional covariates, please keep there open.\n  #CV.MLM=Covariates,\n  #CV.FarmCPU=Covariates,\n  nPC.GLM=3,   ## GLM \u6a21\u578bPC\u6570\n  nPC.MLM=3,   ## MLM \u6a21\u578bPC\u6570\n  nPC.FarmCPU=3, ## FarmCPU\u6a21\u578b\u4e2d\u52a0\u5165\u7684PC\u6570\u91cf\n  ncpus=5,\n  vc.method=\"BRENT\",  ##only works for MLM\uff0c\"EMMA\" or \"HE\" or \"BRENT\"\n  maxLoop=10, ##  FarmCPU \u8fed\u4ee3\u6b21\u6570\n  method.bin=\"static\",   ## \"FaST-LMM\", \"static\" (#only works for FarmCPU)\n  #permutation.threshold=TRUE,\n  #permutation.rep=100,\n  threshold=0.05, # 0.05\/marker size\n  method=c(\"GLM\", \"MLM\", \"FarmCPU\"),\n  file.output=T\n)\n\n#save(imMVP, file = \"imMVP.Rdata\")<\/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-ad25f5c elementor-widget elementor-widget-heading\" data-id=\"ad25f5c\" 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. \u53ef\u89c6\u5316<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-7f17a41 elementor-widget elementor-widget-text-editor\" data-id=\"7f17a41\" 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>\u53ef\u89c6\u5316\u9009\u62e9CMplot\uff0c\u7b80\u5355\u5e76\u4e14\u7f8e\u89c2\uff01<\/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-6760d02 elementor-widget elementor-widget-text-editor\" data-id=\"6760d02\" 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\u5165\u6587\u4ef6\u683c\u5f0f\u5982\u4e0b<\/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-7b01b17 elementor-widget elementor-widget-code-highlight\" data-id=\"7b01b17\" 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># GWAS result dir format\n\nhead Plot_GD10.FarmCPU.txt \nSNP     CHROM   POS     GD10\nSNP1    chr01   20168   0.322959574748127\nSNP2    chr01   20214   0.673619517210625\nSNP3    chr01   20233   0.177721400235444\nSNP4    chr01   20240   0.0547135109062588\nSNP5    chr01   20264   0.725029263883326\nSNP6    chr01   20270   0.0547135109062588\nSNP7    chr01   20337   0.0541283609666494\nSNP8    chr01   20339   0.179058722450606\nSNP9    chr01   20354   0.44060986323047\n\n# Highlight gene list\n\nhead Plot_GD10.FarmCPU_highlight_gene.txt \nSNP2714258\nSNP2714259<\/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-c6490d3 elementor-widget elementor-widget-text-editor\" data-id=\"c6490d3\" 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>\u7ed8\u56fe<\/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-4f0aa19 elementor-widget elementor-widget-code-highlight\" data-id=\"4f0aa19\" 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-r line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-r\">\n\t\t\t\t\t<xmp>library(CMplot)\n\n# Exprot highlight gene list\nGD10_gene_df <- read.table(\"Plot_GD10.FarmCPU_highlight_gene.txt\")\nGD10_gene_vector <- GD10_gene_df$V1\n\n# Exprot GWAS result\nGD10 <- read.table(\"Plot_GD10.FarmCPU.txt\", header = TRUE)\n\n# Manhattan Plot\nCMplot(GD10, plot.type=\"m\",LOG10=TRUE,col=c(\"dodgerblue4\",\"deepskyblue\"),highlight=GD10_gene_vector,\n       highlight.col=rep(c(\"green\"),length=length(GD10_gene_vector)),highlight.cex=1, highlight.text=GD10_gene_vector,      \n       highlight.text.col=rep(\"red\",length(GD10_gene_vector)),threshold=1e-6,threshold.lty=2,   \n       amplify=FALSE,file=\"jpg\",dpi=300,verbose=TRUE,width=14,height=6,highlight.text.cex=1)\n\n# QQplot\nCMplot(GD10,plot.type=\"q\",box=FALSE,file=\"jpg\",file.name=NULL,dpi=300,\n    conf.int=TRUE,conf.int.col=NULL,threshold.col=\"red\",threshold.lty=2,\n    file.output=TRUE,verbose=TRUE,width=5,height=5)\n<\/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-580f98e elementor-widget elementor-widget-image\" data-id=\"580f98e\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img fetchpriority=\"high\" decoding=\"async\" width=\"1024\" height=\"439\" src=\"http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/08\/Rect_Manhtn.GD10-1024x439.jpg\" class=\"attachment-large size-large wp-image-2047\" alt=\"\" srcset=\"http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/08\/Rect_Manhtn.GD10-1024x439.jpg 1024w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/08\/Rect_Manhtn.GD10-300x129.jpg 300w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/08\/Rect_Manhtn.GD10-768x329.jpg 768w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/08\/Rect_Manhtn.GD10-1536x658.jpg 1536w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/08\/Rect_Manhtn.GD10-2048x878.jpg 2048w\" sizes=\"(max-width: 1024px) 100vw, 1024px\" \/>\t\t\t\t\t\t\t\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-30990e8 elementor-widget elementor-widget-image\" data-id=\"30990e8\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img decoding=\"async\" width=\"1024\" height=\"1024\" src=\"http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/08\/GD10.FarmCPU.QQplot-1024x1024.jpg\" class=\"attachment-large size-large wp-image-2051\" alt=\"\" srcset=\"http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/08\/GD10.FarmCPU.QQplot-1024x1024.jpg 1024w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/08\/GD10.FarmCPU.QQplot-300x300.jpg 300w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/08\/GD10.FarmCPU.QQplot-150x150.jpg 150w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/08\/GD10.FarmCPU.QQplot-768x768.jpg 768w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/08\/GD10.FarmCPU.QQplot-1536x1536.jpg 1536w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/08\/GD10.FarmCPU.QQplot.jpg 1650w\" sizes=\"(max-width: 1024px) 100vw, 1024px\" \/>\t\t\t\t\t\t\t\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>0.\u524d\u8a00 \u4f5c\u4e3a\u4e00\u4e2a\u57fa\u56e0\u7ec4\u5b66\u7814\u7a76\u4eba\u5458\uff0c\u600e\u4e48\u53ef\u4ee5\u4e0d\u4f1aGWAS\u5462\uff1f\u6700\u8fd1\u63a5\u4e86\u4e00\u4e2aGWAS\u7684\u9879\u76ee\uff0c\u6b63\u597d\u501f\u7740\u8fd9\u4e2a\u673a\u4f1a\u8fb9\u505a\u8fb9 &#8230; <a title=\"GWAS\u5b66\u4e60\" class=\"read-more\" href=\"http:\/\/www.majunpeng.com\/index.php\/2025\/08\/24\/gwas%e5%ad%a6%e4%b9%a0\/\" aria-label=\"\u9605\u8bfb GWAS\u5b66\u4e60\">\u9605\u8bfb\u66f4\u591a<\/a><\/p>\n","protected":false},"author":1,"featured_media":1939,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_crdt_document":"","footnotes":""},"categories":[6],"tags":[],"class_list":["post-1938","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\/ 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