{"id":56018,"date":"2024-06-16T17:24:05","date_gmt":"2024-06-16T09:24:05","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=56018"},"modified":"2024-06-16T17:24:05","modified_gmt":"2024-06-16T09:24:05","slug":"%e6%90%ad%e5%bb%ba%e7%94%9f%e4%bf%a1%e5%88%86%e6%9e%90%e6%b5%81%e6%b0%b4%e7%ba%bf%ef%bc%8c%e5%a6%82%e5%b7%a5%e5%8e%82%e4%b8%80%e6%a0%b724%e5%b0%8f%e6%97%b6%e8%bf%90%e8%bd%acsnakemake-2","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=56018","title":{"rendered":"\u642d\u5efa\u751f\u4fe1\u5206\u6790\u6d41\u6c34\u7ebf\uff0c\u5982\u5de5\u5382\u4e00\u683724\u5c0f\u65f6\u8fd0\u8f6cSnakemake\u2014\u2014\u8fdb\u9636\u547d\u4ee4"},"content":{"rendered":"


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14px;\">\u6307\u5b9a\u6d41\u7a0b\u7684\u7ebf\u7a0b\u6570\u53caCPU\u5185\u6838\u6570\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u4e3a\u6d41\u7a0b\u6dfb\u52a0\u914d\u7f6e\u6587\u4ef6\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u5f15\u5165\u8f93\u5165\u6587\u4ef6\u7684\u51fd\u6570\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u6dfb\u52a0\u89c4\u5219\u53c2\u6570\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u4e3a\u6d41\u7a0b\u6dfb\u52a0\u65e5\u5fd7\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u8bbe\u7f6e\u8f93\u51fa\u6587\u4ef6\u4e3a\u4e34\u65f6\u6587\u4ef6\u6216\u8005\u4fdd\u62a4\u6587\u4ef6<\/span><span style=\"\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\"><br \/><\/span><\/p>\n<h2 style=\"text-align: center;\"><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><em><span style=\"font-size: 20px;\"><strong style=\"text-align: justify;letter-spacing: 0.034em;\"><span style=\"color: rgb(51, 51, 51);\">1. \u6307\u5b9a\u6d41\u7a0b\u7ebf\u7a0b\u6570<\/span><\/strong><\/span><\/em><\/span><strong><span style=\"font-family: Calibri;font-size: 16pt;\"><o:p><\/o:p><\/span><\/strong><\/h2>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u5bf9\u4e8e\u751f\u4fe1\u7684\u67d0\u4e9b\u5de5\u5177\uff0c\u5c0f\u679c\u5efa\u8bae\u4f7f\u7528\u591a\u4e2a\u7ebf\u7a0b\u4ee5\u52a0\u5feb\u8ba1\u7b97\u901f\u5ea6\u3002\u8be5\u5982\u4f55\u5b9e\u73b0\u5462\uff1f\u6211\u4eec\u53ef\u4ee5\u901a\u8fc7threads\u6307\u4ee4\u8ba9Snakemake\u77e5\u9053\u89c4\u5219\u9700\u8981\u7684\u7ebf\u7a0b\u3002\u4f8b\u5982\uff1a<\/span><\/p>\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<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"nginx\"><code><span class=\"code-snippet_outer\">rule bwa_map:<\/span><\/code><code><span class=\"code-snippet_outer\"> input:<\/span><\/code><code><span class=\"code-snippet_outer\"> \"data\/genome.fa\",<\/span><\/code><code><span class=\"code-snippet_outer\"> \"data\/samples\/{sample}.fastq\"<\/span><\/code><code><span class=\"code-snippet_outer\"> output:<\/span><\/code><code><span class=\"code-snippet_outer\"> \"mapped_reads\/{sample}.bam\"<\/span><\/code><code><span class=\"code-snippet_outer\"> threads: 8<\/span><\/code><code><span class=\"code-snippet_outer\"> shell:<\/span><\/code><code><span class=\"code-snippet_outer\"> \"bwa mem -t {threads} {input} | samtools view -Sb - > {output}\"<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u6dfb\u52a0\u4e00\u884c\u547d\u4ee4\uff0c\u5c31\u53ef\u4ee5\u6307\u5b9arule bwa_map\u4f7f\u75288\u4e2a\u7ebf\u7a0b\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u503c\u5f97\u4e00\u63d0\u7684\u662fsnakemake\u4f1a\u786e\u4fdd\u540c\u65f6\u8fd0\u884c\u7684\u6240\u6709\u4f5c\u4e1a\u7684\u7ebf\u7a0b\u603b\u6570\uff0c\u4e0d\u8d85\u8fc7\u7ed9\u5b9a\u6570\u91cf\u7684CPU\u5185\u6838\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u6211\u4eec\u5728\u6267\u884csnakemake\u5de5\u4f5c\u6d41\u7a0b\u65f6\uff0c\u4f7f\u7528–cores\u53c2\u6570\uff0c\u6307\u5b9a\u4f7f\u7528\u7684CPU\u5185\u6838\u6570\u91cf\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"color: rgb(51, 51, 51);font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\"><o:p><\/o:p><\/span><\/p>\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=\"nginx\"><code><span class=\"code-snippet_outer\">snakemake --cores 10<\/span><\/code><\/pre>\n<\/section>\n<p><br \/><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\">\u6bd4\u5982\u8fd9\u6761\u547d\u4ee4\uff0c\u5c31\u4f1a\u752810\u4e2aCPU\u5185\u6838\u6267\u884c\u8be5\u5de5\u4f5c\u6d41\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\">rule bwa_map\u6307\u5b9a\u4e868\u4e2a\u7ebf\u7a0b\uff0c\u90a3\u4e48snakemake\u5c31\u4f1a\u7528\u5269\u4e0b\u4e24\u4e2a\u5185\u6838\u53bb\u6267\u884c\u5176\u4ed6\u7684\u4efb\u52a1\uff0c\u4f8b\u5982samtools_sort\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\">\u5f53\u63d0\u4f9b\u7684\u5185\u6838\u5c11\u4e8e\u7ebf\u7a0b\u65f6\uff0c\u89c4\u5219\u4f7f\u7528\u7684\u7ebf\u7a0b\u6570\u5c06\u51cf\u5c11\u5230\u7ed9\u5b9a\u5185\u6838\u6570\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\">\u5982\u679c\u7ed9\u51fa\u7684–cores\u6ca1\u6709\u6570\u5b57\uff0c\u5219\u4f7f\u7528\u6240\u6709\u53ef\u7528\u7684cores\u3002<\/span><span style=\"\"><o:p><\/o:p><\/span><\/p>\n<p style=\"text-align: center;\"><br \/><\/p>\n<h2 style=\"text-align: center;\"><strong><em><span style=\"font-size: 20px;\">2. \u8bbe\u7f6e\u914d\u7f6e\u6587\u4ef6<\/span><\/em><\/strong><strong><span style=\"font-family: \u5b8b\u4f53;font-size: 16pt;\"><o:p><\/o:p><\/span><\/strong><\/h2>\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<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"makefile\"><code><span class=\"code-snippet_outer\">SAMPLES = [\"A\", \"B\"]<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">rule bcftools_call:<\/span><\/code><code><span class=\"code-snippet_outer\"> input:<\/span><\/code><code><span class=\"code-snippet_outer\"> fa=\"data\/genome.fa\",<\/span><\/code><code><span class=\"code-snippet_outer\"> bam=expand(\"sorted_reads\/{sample}.bam\", sample=SAMPLES),<\/span><\/code><code><span class=\"code-snippet_outer\"> bai=expand(\"sorted_reads\/{sample}.bam.bai\", sample=SAMPLES)<\/span><\/code><code><span class=\"code-snippet_outer\"> output:<\/span><\/code><code><span class=\"code-snippet_outer\"> \"calls\/all.vcf\"<\/span><\/code><code><span class=\"code-snippet_outer\"> shell:<\/span><\/code><code><span class=\"code-snippet_outer\"> \"bcftools mpileup -f {input.fa} {input.bam} | \"<\/span><\/code><code><span class=\"code-snippet_outer\"> \"bcftools call -mv - > {output}\"<\/span><\/code><\/pre>\n<\/section>\n<p><br \/><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\">\u4e0a\u671f\u8bb2\u89e3\u4e2d\u6211\u4eec\u4f7f\u7528<span style=\"color: rgb(64, 64, 64);letter-spacing: 0pt;\">SAMPLES\u5217\u8868<\/span>\uff0c\u6765\u5339\u914d\u6240\u6709\u6211\u4eec\u9700\u8981\u5904\u7406\u7684\u6587\u4ef6\u3002A\uff0cB\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\">\u4f46\u662f\uff0c\u5f53\u65b0\u7684\u6570\u636e\u6765\u4e86\u9700\u8981\u6211\u4eec\u7684\u6d41\u7a0b\u5206\u6790\u65f6\uff0c\u9700\u8981\u624b\u52a8\u5730\u66f4\u6539\uff0c\u96be\u4ee5\u9002\u5e94\u65b0\u7684\u6570\u636e\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">Snakemake\u8003\u8651\u5230\u4e86\u8fd9\u79cd\u60c5\u51b5\uff0c\u5b83\u63d0\u4f9b\u4e86\u4e00\u79cd\u914d\u7f6e\u6587\u4ef6\u673a\u5236\u3002\u914d\u7f6e\u6587\u4ef6\u53ef\u4ee5\u7528JSON\u6216YAML\u7f16\u5199\uff0c\u5e76\u4e0e\u6307\u4ee4\u4e00\u8d77\u4f7f\u7528\u3002<\/span><span style=\"\"><o:p><\/o:p><\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\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=\"javascript\"><code><span class=\"code-snippet_outer\">configfile: \"config.yaml\"<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;\"><br \/><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u6211\u4eec\u53ea\u9700\u8981\u5728\u5de5\u4f5c\u6d41\u7684\u9876\u7aef\u6dfb\u52a0\u8fd9\u4e00\u884c\u547d\u4ee4\u3002Snakemake\u5c06\u52a0\u8f7d\u914d\u7f6e\u6587\u4ef6\uff0c\u5e76\u5c06\u5176\u5185\u5bb9\u5b58\u50a8\u5230\u540d\u4e3a\u7684\u5168\u5c40\u53ef\u7528\u5b57\u5178\u4e2d\u3002<\/span><span style=\"\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u6211\u4eec\u521b\u5efa\u4e00\u4e2aconfig.yaml\u6587\u4ef6\uff0c\u7f16\u5199samples\u7684\u6587\u4ef6\u8def\u5f84<\/span><span style=\"\"><o:p><\/o:p><\/span><\/p>\n<p style=\"white-space: normal;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\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<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"http\"><code><span class=\"code-snippet_outer\">samples: <\/span><\/code><code><span class=\"code-snippet_outer\"> A: data\/samples\/A.fastq <\/span><\/code><code><span class=\"code-snippet_outer\">  B: data\/samples\/B.fastq<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u73b0\u5728\u6211\u4eec\u5c31\u53ef\u4ee5\u53bb\u6389<span style=\"color: rgb(64, 64, 64);letter-spacing: 0pt;\">SAMPLES\u5217\u8868\uff0c\u5e76\u5c06rule\u6539\u4e3a<\/span><\/span><span style=\"font-family: \u5b8b\u4f53;color: rgb(64, 64, 64);letter-spacing: 0pt;font-size: 9pt;\"><o:p><\/o:p><\/span><\/p>\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<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"nginx\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attribute\">rule<\/span> bcftools_call:<\/span><\/code><code><span class=\"code-snippet_outer\"> input:<\/span><\/code><code><span class=\"code-snippet_outer\"> fa=<span class=\"code-snippet__string\">\"data\/genome.fa\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> bam=expand(<span class=\"code-snippet__string\">\"sorted_reads\/{sample}.bam\"<\/span>, sample=config[<span class=\"code-snippet__string\">\"samples\"<\/span>]),<\/span><\/code><code><span class=\"code-snippet_outer\"> bai=expand(<span class=\"code-snippet__string\">\"sorted_reads\/{sample}.bam.bai\"<\/span>, sample=config[<span class=\"code-snippet__string\">\"samples\"<\/span>])<\/span><\/code><code><span class=\"code-snippet_outer\"> output:<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__string\">\"calls\/all.vcf\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> shell:<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__string\">\"bcftools mpileup -f {input.fa} {input.bam} | \"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__string\">\"bcftools call -mv - > {output}\"<\/span><\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: center;white-space: normal;\"><br \/><\/p>\n<h2 style=\"text-align: center;\"><strong><em><span style=\"font-size: 20px;\">3. \u5b9a\u4e49\u8f93\u5165\u51fd\u6570<\/span><\/em><\/strong><\/h2>\n<\/section>\n<p><span style=\"font-size: 14px;\"><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;color: rgb(51, 51, 51);letter-spacing: 0pt;\">\u6211\u4eec\u5df2\u7ecf\u5c06sample\u6587\u4ef6\u7684\u8def\u5f84\u5b58\u50a8\u5728\u914d\u7f6e\u6587\u4ef6\u4e2d\uff0c\u56e0\u6b64\u6211\u4eec\u8fd8\u53ef\u4ee5\u5b9a\u4e49\u4e00\u4e2a\u51fd\u6570\u6765\u4e3a\u4f7f\u7528\u8fd9\u4e9b\u8def\u5f84\u3002<\/span><span style=\"color: rgb(51, 51, 51);letter-spacing: 0pt;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><o:p><\/o:p><\/span><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">Snakemake \u5de5\u4f5c\u6d41\u7684\u6267\u884c\u5206\u4e3a\u4e09\u4e2a\u9636\u6bb5\u3002\u5206\u522b\u662f<o:p><\/o:p><\/span><\/p>\n<p style=\"margin-right: 0pt;margin-left: 0pt;\"><span style=\"color: rgb(51, 51, 51);letter-spacing: 0pt;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">1.\u5728\u521d\u59cb\u5316\u9636\u6bb5\uff0c\u5c06\u89e3\u6790\u5b9a\u4e49\u5de5\u4f5c\u6d41\u7684\u6587\u4ef6\uff0c\u5e76\u5b9e\u4f8b\u5316\u6240\u6709\u89c4\u5219\u3002<o:p><\/o:p><\/span><\/p>\n<p style=\"margin-right: 0pt;margin-left: 0pt;\"><span style=\"color: rgb(51, 51, 51);letter-spacing: 0pt;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">2.\u5728DAG\u9636\u6bb5\uff0c\u901a\u8fc7\u586b\u5145\u901a\u914d\u7b26\u5e76\u5c06\u8f93\u5165\u6587\u4ef6\u4e0e\u8f93\u51fa\u6587\u4ef6\u5339\u914d\uff0c\u53ef\u4ee5\u6784\u5efa\u6240\u6709\u4f5c\u4e1a\u7684\u6709\u5411\u65e0\u5faa\u73af\u4f9d\u8d56\u56fe\u3002<o:p><\/o:p><\/span><\/p>\n<p style=\"margin-right: 0pt;margin-left: 0pt;\"><span style=\"color: rgb(51, 51, 51);letter-spacing: 0pt;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">3.\u5728\u8c03\u5ea6\u9636\u6bb5\uff0c\u6267\u884c\u4f5c\u4e1a\u7684DAG\uff0c\u6839\u636e\u53ef\u7528\u8d44\u6e90\u542f\u52a8\u4f5c\u4e1a\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u5728\u521d\u59cb\u5316\u9636\u6bb5\uff0c\u8f93\u5165\u6587\u4ef6\u7684\u51fd\u6570\u4f1a\u88ab\u6267\u884c\uff0c\u4f46\u662f\u5728\u8fd9\u4e2a\u9636\u6bb5<span style=\"color: rgb(51, 51, 51);letter-spacing: 0pt;\">\u4f5c\u4e1a\u3001\u901a\u914d\u7b26\u503c\u548c\u89c4\u5219\u4f9d\u8d56\u5173\u7cfb\u8fd8\u4e0d\u77e5\u9053\u3002<\/span><o:p><\/o:p><\/span><\/p>\n<p><span style=\"color: rgb(51, 51, 51);letter-spacing: 0pt;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u6211\u4eec\u9700\u8981\u5c06\u8f93\u5165\u6587\u4ef6\u7684\u786e\u5b9a\u63a8\u8fdf\u5230DAG\u9636\u6bb5\u3002\u8fd9\u53ef\u4ee5\u901a\u8fc7\u5728\u8f93\u5165\u6307\u4ee4\u4e2d\u6307\u5b9a\u8f93\u5165\u51fd\u6570\u800c\u4e0d\u662f\u5b57\u7b26\u4e32\u6765\u5b9e\u73b0\u3002\u5bf9\u4e8e\u89c4\u5219\uff0c\u5176\u5de5\u4f5c\u539f\u7406\u5982\u4e0b\uff1a<\/span><span style=\"font-family: Helvetica;color: rgb(51, 51, 51);letter-spacing: 0pt;font-size: 7.5pt;\"><o:p><\/o:p><\/span><\/p>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\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<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"python\"><code><span class=\"code-snippet_outer\">def get_bwa_map_input_fastqs(wildcards):<\/span><\/code><code><span class=\"code-snippet_outer\"> return config[\"samples\"][wildcards.sample]<\/span><\/code><code><span class=\"code-snippet_outer\">\u5b9a\u4e49\u4e00\u4e2a\u83b7\u53d6\u8f93\u5165\u6587\u4ef6\u8def\u5f84\u7684\u51fd\u6570\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">rule bwa_map:<\/span><\/code><code><span class=\"code-snippet_outer\"> input:<\/span><\/code><code><span class=\"code-snippet_outer\"> \"data\/genome.fa\",<\/span><\/code><code><span class=\"code-snippet_outer\"> get_bwa_map_input_fastqs #\u8c03\u7528\u8f93\u5165\u51fd\u6570<\/span><\/code><code><span class=\"code-snippet_outer\"> output:<\/span><\/code><code><span class=\"code-snippet_outer\"> \"mapped_reads\/{sample}.bam\"<\/span><\/code><code><span class=\"code-snippet_outer\"> threads: 8<\/span><\/code><code><span class=\"code-snippet_outer\"> shell:<\/span><\/code><code><span class=\"code-snippet_outer\">        \"bwa mem -t {threads} {input} | samtools view -Sb - > {output}\"<\/span><\/code><\/pre>\n<\/section>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><span style=\"color: rgb(51, 51, 51);letter-spacing: 0pt;\">\u8fd9\u4e2a\u51fd\u6570\u4f1a\u8fd4\u56de\u8f93\u5165\u6587\u4ef6\u7684\u8def\u5f84\uff0c<\/span><span style=\"color: rgb(64, 64, 64);letter-spacing: 0pt;\">[wildcards<\/span><span style=\"color: rgb(102, 102, 102);letter-spacing: 0pt;\">.<\/span><span style=\"color: rgb(64, 64, 64);letter-spacing: 0pt;\">sample]\u901a\u8fc7\u8fd9\u4e2a\u547d\u4ee4\u53ef\u4ee5\u8fd4\u56de\u6587\u4ef6<\/span><\/span><\/p>\n<p style=\"white-space: normal;\"><br \/><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">4. \u8bbe\u7f6e\u89c4\u5219\u7684\u53c2\u6570<\/span><\/em><\/strong><\/p>\n<p style=\"text-align: center;white-space: normal;font-size: 16px;\"><o:p><\/o:p><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;color: rgb(51, 51, 51);letter-spacing: 0pt;\">\u6709\u65f6\uff0cshell\u547d\u4ee4\u4e0d\u4ec5\u4ec5\u7531\u8f93\u5165\u548c\u8f93\u51fa\u6587\u4ef6\u4ee5\u53ca\u4e00\u4e9b\u9759\u6001\u6807\u5fd7\u7ec4\u6210\u3002\u6709\u65f6\u5019\u53ef\u80fd\u9700\u8981\u6839\u636e\u4f5c\u4e1a\u7684\u901a\u914d\u7b26\u503c\u8bbe\u7f6e\u5176\u4ed6\u53c2\u6570\u3002Snakemake\u5141\u8bb8\u4f7f\u7528\u6307\u4ee4params\u4e3a\u89c4\u5219\u5b9a\u4e49\u4efb\u610f\u53c2\u6570\u3002\u4f8b\u5982<\/span><span style=\"font-family: \u5b8b\u4f53;color: rgb(51, 51, 51);letter-spacing: 0pt;font-size: 7.5pt;\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:"yes";font-family:"Open Sans";mso-fareast-font-family:\u5b8b\u4f53;color:rgb(51,51,51);font-size:12.0000pt;mso-font-kerning:0.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\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<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"python\"><code><span class=\"code-snippet_outer\">rule bwa_map:<\/span><\/code><code><span class=\"code-snippet_outer\"> input:<\/span><\/code><code><span class=\"code-snippet_outer\"> \"data\/genome.fa\",<\/span><\/code><code><span class=\"code-snippet_outer\"> get_bwa_map_input_fastqs<\/span><\/code><code><span class=\"code-snippet_outer\"> output:<\/span><\/code><code><span class=\"code-snippet_outer\"> \"mapped_reads\/{sample}.bam\"<\/span><\/code><code><span class=\"code-snippet_outer\"> params:<\/span><\/code><code><span class=\"code-snippet_outer\"> rg=r\"@RGtID:{sample}tSM:{sample}\"<\/span><\/code><code><span class=\"code-snippet_outer\"> threads: 8<\/span><\/code><code><span class=\"code-snippet_outer\"> shell:<\/span><\/code><code><span class=\"code-snippet_outer\">        \"bwa mem -R '{params.rg}' -t {threads} {input} | samtools view -Sb - > {output}\"<\/span><\/code><\/pre>\n<\/section>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<p><span style=\"font-size: 14px;\"><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;color: rgb(51, 51, 51);letter-spacing: 0pt;\">\u7a81\u53d8\u5206\u6790\u4f1a\u8003\u8651\u5f88\u591a\u53c2\u6570\u3002\u4e00\u4e2a\u7279\u522b\u91cd\u8981\u7684\u662f\u5148\u524d\u7684\u7a81\u53d8\u7387\uff08\u9ed8\u8ba4\u4e3a1e-3\uff09\u3002<\/span><span style=\"color: rgb(51, 51, 51);letter-spacing: 0pt;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><o:p><\/o:p><\/span><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;color: rgb(51, 51, 51);letter-spacing: 0pt;font-size: 14px;\">\u6211\u4eec\u53ef\u4ee5\u5411\u914d\u7f6e\u6587\u4ef6\u4e2d\u6dfb\u52a0\u4e00\u4e2akey\u5e76\u4f7f\u7528\u89c4\u5219\u4e2d\u7684\u6307\u4ee4,\u5c06\u5176\u8c03\u7528\u5230shell\u547d\u4ee4\u6765\u914d\u7f6e\u8fd9\u4e2akey\u3002<\/span><span style=\"font-family: \u5b8b\u4f53;color: rgb(51, 51, 51);letter-spacing: 0pt;font-size: 7.5pt;\"><o:p><\/o:p><\/span><\/p>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p style=\"text-align: center;\"><br \/><\/p>\n<p style=\"text-align: center;white-space: normal;\"><strong><em><span style=\"font-size: 20px;\">5.\u65e5\u5fd7<\/span><\/em><\/strong><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><span style=\"color: rgb(51, 51, 51);letter-spacing: 0pt;\">\u5728\u6267\u884c\u4e00\u4e2a\u5927\u578b\u5de5\u4f5c\u6d41\u65f6\uff0c\u901a\u5e38\u9700\u8981\u5c06\u6bcf\u4e2a\u4f5c\u4e1a\u7684\u65e5\u5fd7\u8bb0\u5f55\u8f93\u51fa\u5b58\u50a8\u5230\u4e00\u4e2a\u5355\u72ec\u7684\u6587\u4ef6\u4e2d\uff0c\u800c\u4e0d\u662f\u5728\u591a\u4e2a\u4f5c\u4e1a\u5e76\u884c\u8fd0\u884c\u65f6\u5c06\u6240\u6709\u65e5\u5fd7\u8bb0\u5f55\u8f93\u51fa\u6253\u5370\u5230\u7ec8\u7aef\uff0c\u8fd9\u4f1a\u5bfc\u81f4\u8f93\u51fa\u6df7\u4e71\u3002\u4e3a\u6b64\uff0cSnakemake\u5141\u8bb8\u4e3a\u89c4\u5219\u6307\u5b9a\u65e5\u5fd7\u6587\u4ef6\u3002\u53ef\u4ee5\u901a\u8fc7\u6dfb\u52a0log\u547d\u4ee4\u6765\u5b8c\u6210<\/span>\u3002<\/span><span style=\"\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"mso-spacerun:"yes";font-family:"Open Sans";mso-fareast-font-family:\u5b8b\u4f53;color:rgb(51,51,51);font-size:12.0000pt;mso-font-kerning:0.0000pt;\"><o:p><\/o:p><\/span><\/p>\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<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"python\"><code><span class=\"code-snippet_outer\">rule bwa_map:<\/span><\/code><code><span class=\"code-snippet_outer\"> input:<\/span><\/code><code><span class=\"code-snippet_outer\"> \"data\/genome.fa\",<\/span><\/code><code><span class=\"code-snippet_outer\"> get_bwa_map_input_fastqs<\/span><\/code><code><span class=\"code-snippet_outer\"> output:<\/span><\/code><code><span class=\"code-snippet_outer\"> \"mapped_reads\/{sample}.bam\"<\/span><\/code><code><span class=\"code-snippet_outer\"> params:<\/span><\/code><code><span class=\"code-snippet_outer\"> rg=r\"@RGtID:{sample}tSM:{sample}\"<\/span><\/code><code><span class=\"code-snippet_outer\"> log:<\/span><\/code><code><span class=\"code-snippet_outer\"> \"logs\/bwa_mem\/{sample}.log\"<\/span><\/code><code><span class=\"code-snippet_outer\"> threads: 8<\/span><\/code><code><span class=\"code-snippet_outer\"> shell:<\/span><\/code><code><span class=\"code-snippet_outer\"> \"(bwa mem -R '{params.rg}' -t {threads} {input} | \"<\/span><\/code><code><span class=\"code-snippet_outer\"> \"samtools view -Sb - > {output}) 2> {log}\"<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\">\u6267\u884cshell\u547d\u4ee4\u65f6\uff0c\u53ef\u4ee5\u901a\u8fc7\u7ba1\u9053\u4f20\u8f93\u5230\u65e5\u5fd7\u6587\u4ef6\u4e2d\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;white-space: normal;font-size: 16px;\"><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><strong><em><span style=\"font-size: 20px;\">6.\u4e34\u65f6\u6587\u4ef6\u548c\u4fdd\u62a4\u6587\u4ef6<\/span><\/em><\/strong><\/span><strong style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;letter-spacing: 0.034em;\"><em><span style=\"font-size: 20px;\">\u200d<\/span><\/em><\/strong><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u5f53\u6211\u4eec\u8fd0\u884c\u4e00\u4e2a\u5927\u578b\u5de5\u4f5c\u6d41\u65f6\uff0c\u4f1a\u4ea7\u751f\u8bb8\u591a\u4e2d\u95f4\u6587\u4ef6\uff0c\u8fd9\u4e9b\u6587\u4ef6\u4f1a\u5360\u7528\u5927\u91cf\u7684\u78c1\u76d8\u7a7a\u95f4\uff0c\u5e76\u4e14\u4e5f\u9700\u8981\u8017\u8d39\u8ba1\u7b97\u8d44\u6e90\u548c\u65f6\u95f4\u3002\u4e3a\u4e86\u907f\u514d\u8fd9\u79cd\u60c5\u51b5\u53ef\u4ee5\u5c06\u8f93\u51fa\u6587\u4ef6\u8bbe\u7f6e\u4e3a\u4e34\u65f6\u6587\u4ef6\uff0c\u4e00\u65e6\u9700\u8981\u5b83\u7684\u4f5c\u4e1a\u6267\u884c\u5b8c\u6bd5\uff0c\u5c31\u4f1a\u5220\u9664\u8fd9\u4e2a\u4e34\u65f6\u6587\u4ef6\uff0c\u907f\u514d\u78c1\u76d8\u5360\u7528\u8fc7\u591a\u3002<\/span><span style=\"\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"color: rgb(51, 51, 51);font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><\/span><span style=\"mso-spacerun:"yes";font-family:"Open Sans";mso-fareast-font-family:\u5b8b\u4f53;color:rgb(51,51,51);font-size:12.0000pt;mso-font-kerning:0.0000pt;\"><o:p><\/o:p><\/span><\/p>\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<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"python\"><code><span class=\"code-snippet_outer\">rule bwa_map:<\/span><\/code><code><span class=\"code-snippet_outer\"> input:<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__string\">\"data\/genome.fa\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> get_bwa_map_input_fastqs<\/span><\/code><code><span class=\"code-snippet_outer\"> output:<\/span><\/code><code><span class=\"code-snippet_outer\"> temp(<span class=\"code-snippet__string\">\"mapped_reads\/{sample}.bam\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"> params:<\/span><\/code><code><span class=\"code-snippet_outer\"> rg=<span class=\"code-snippet__string\">r\"@RGtID:{sample}tSM:{sample}\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> log:<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__string\">\"logs\/bwa_mem\/{sample}.log\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> threads: <span class=\"code-snippet__number\">8<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> shell:<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__string\">\"(bwa mem -R '{params.rg}' -t {threads} {input} | \"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__string\">\"samtools view -Sb - > {output}) 2> {log}\"<\/span><\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-size: 14px;\">\u6709\u7684\u65f6\u5019\uff0c\u6211\u4eec\u5df2\u7ecf\u6267\u884c\u5b8c\u4e86\u5de5\u4f5c\u6d41\u7a0b\uff0c\u5f97\u5230\u4e86\u60f3\u8981\u7684\u7ed3\u679c\uff0c\u4e0d\u5e0c\u671b\u7ed3\u679c\u906d\u5230\u7be1\u6539\u3002\u6211\u4eec\u53ef\u4ee5\u5c06\u7ed3\u679c\u95ee\u4ef7\u4f60\u8bbe\u7f6e\u4e3a\u4fdd\u62a4\u6587\u4ef6\u3002Snakemake\u4f1a\u5bf9\u6587\u4ef6\u7cfb\u7edf\u4e2d\u7684\u8f93\u51fa\u6587\u4ef6\u8fdb\u884c\u5199\u4fdd\u62a4\uff0c\u8fd9\u6837\u5c31\u4e0d\u4f1a\u610f\u5916\u5730\u8986\u76d6\u6216\u5220\u9664\u5b83\u3002<span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><o:p><\/o:p><\/span><\/span><\/p>\n<p><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;white-space: normal;font-size: 16px;\"><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><strong><em><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 20px;\">\u6d41\u7a0b\u603b\u7ed3<\/span><\/em><\/strong><\/span><\/p>\n<\/section>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u521b\u5efa\u914d\u7f6e\u6587\u4ef6<\/span><span style=\"\"><o:p><\/o:p><\/span><\/p>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\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<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"http\"><code><span class=\"code-snippet_outer\">samples: <\/span><\/code><code><span class=\"code-snippet_outer\">A: data\/samples\/A.fastq <\/span><\/code><code><span class=\"code-snippet_outer\">B: data\/samples\/B.fastq<\/span><\/code><code><span class=\"code-snippet_outer\">prior_mutation_rate: 0.001<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">Snakemake\u5de5\u4f5c\u6d41\u7a0b\u6587\u4ef6Snakefile<\/span><\/p>\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<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"http\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attribute\">configfile<\/span>: \"config.yaml\" #\u6307\u5b9a\u914d\u7f6e\u6587\u4ef6<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">rule all:<\/span><\/code><code><span class=\"code-snippet_outer\"> input:<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__string\">\"plots\/quals.svg\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__function\"><span class=\"code-snippet__keyword\">def<\/span> <span class=\"code-snippet__title\">get_bwa_map_input_fastqs<\/span><span class=\"code-snippet__params\">(wildcards)<\/span>:<\/span> <span class=\"code-snippet__comment\">#\u5b9a\u4e49\u8f93\u5165\u51fd\u6570<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__keyword\">return<\/span> config[<span class=\"code-snippet__string\">\"samples\"<\/span>][wildcards.sample]<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">rule bwa_map:<\/span><\/code><code><span class=\"code-snippet_outer\"> input:<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__string\">\"data\/genome.fa\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> get_bwa_map_input_fastqs<\/span><\/code><code><span class=\"code-snippet_outer\"> output:<\/span><\/code><code><span class=\"code-snippet_outer\"> temp(<span class=\"code-snippet__string\">\"mapped_reads\/{sample}.bam\"<\/span>)<span class=\"code-snippet__comment\">#\u8bbe\u7f6e\u4e34\u65f6\u6587\u4ef6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> params:<\/span><\/code><code><span class=\"code-snippet_outer\"> rg=<span class=\"code-snippet__string\">r\"@RGtID:{sample}tSM:{sample}\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> log:<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__string\">\"logs\/bwa_mem\/{sample}.log\"<\/span> <span class=\"code-snippet__comment\">#\u8f93\u51fa\u65e5\u5fd7<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> threads: <span class=\"code-snippet__number\">8<\/span> <span class=\"code-snippet__comment\">#\u8bbe\u5b9a\u7ebf\u7a0b<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> shell:<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__string\">\"(bwa mem -R '{params.rg}' -t {threads} {input} | \"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__string\">\"samtools view -Sb - > {output}) 2> {log}\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">rule samtools_sort:<\/span><\/code><code><span class=\"code-snippet_outer\"> input:<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__string\">\"mapped_reads\/{sample}.bam\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> output:<\/span><\/code><code><span class=\"code-snippet_outer\"> protected(<span class=\"code-snippet__string\">\"sorted_reads\/{sample}.bam\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"> shell:<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__string\">\"samtools sort -T sorted_reads\/{wildcards.sample} \"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__string\">\"-O bam {input} > {output}\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">rule samtools_index:<\/span><\/code><code><span class=\"code-snippet_outer\"> input:<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__string\">\"sorted_reads\/{sample}.bam\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> output:<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__string\">\"sorted_reads\/{sample}.bam.bai\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> shell:<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__string\">\"samtools index {input}\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">rule bcftools_call:<\/span><\/code><code><span class=\"code-snippet_outer\"> input:<\/span><\/code><code><span class=\"code-snippet_outer\"> fa=<span class=\"code-snippet__string\">\"data\/genome.fa\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"> bam=expand(<span class=\"code-snippet__string\">\"sorted_reads\/{sample}.bam\"<\/span>, sample=config[<span class=\"code-snippet__string\">\"samples\"<\/span>]),<\/span><\/code><code><span class=\"code-snippet_outer\"> bai=expand(<span class=\"code-snippet__string\">\"sorted_reads\/{sample}.bam.bai\"<\/span>, sample=config[<span class=\"code-snippet__string\">\"samples\"<\/span>])<\/span><\/code><code><span class=\"code-snippet_outer\"> output:<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__string\">\"calls\/all.vcf\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> params:<\/span><\/code><code><span class=\"code-snippet_outer\"> rate=config[<span class=\"code-snippet__string\">\"prior_mutation_rate\"<\/span>]<\/span><\/code><code><span class=\"code-snippet_outer\"> log:<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__string\">\"logs\/bcftools_call\/all.log\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> shell:<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__string\">\"(bcftools mpileup -f {input.fa} {input.bam} | \"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__string\">\"bcftools call -mv -P {params.rate} - > {output}) 2> {log}\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">rule plot_quals:<\/span><\/code><code><span class=\"code-snippet_outer\"> input:<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__string\">\"calls\/all.vcf\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> output:<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__string\">\"plots\/quals.svg\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> script:<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__string\">\"scripts\/plot-quals.py\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: center;\"><br \/><\/p>\n<p><strong><span style=\"font-family: \u5b8b\u4f53;\"><span style=\"font-family:\u5b8b\u4f53;\">\u597d\u4e86\u5c0f\u679c\u4eca\u5929\u7684\u8bb2\u89e3\u5c31\u5230\u8fd9\u91cc\u4e86\uff0c\u4e0b\u671f\u518d\u89c1<\/span><span style=\"font-family:Calibri;\">~<\/span><\/span><\/strong><strong><span style=\"font-family: \u5b8b\u4f53;\"><o:p><\/o:p><\/span><\/strong><\/p>\n<p style=\"text-align: center;\"><br \/><\/p>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<p><span style=\"color: rgb(217, 33, 66);font-size: 10.5pt;font-family: \u5fae\u8f6f\u96c5\u9ed1;\">\u5176\u4ed6\u76f8\u5173\u5206\u6790\u5185\u5bb9\uff0c\u4f8b\u5982\u9884\u6d4b\u80bf\u7624\u6837\u672c\u836f\u7269\u654f\u611f\u6027\u5206\u6790(http:\/\/www.biocloudservice.com\/712\/712.php),\u9884\u6d4b\u67d0\u6837\u672c\u4e9a\u578b\u5bf9\u514d\u75ab\u6cbb\u7597\u7684\u53cd\u5e94(http:\/\/www.biocloudservice.com\/292\/292.php)\uff0c\u5355\u6837\u672c\u5bcc\u96c6\u7b97\u6cd5\u5206\u6790\u514d\u75ab\u6d78\u6da6\u4e30\u5ea6(http:\/\/www.biocloudservice.com\/106\/106.php)\uff0c\u8ba1\u7b9764\u79cd\u514d\u75ab\u7ec6\u80de\u76f8\u5bf9\u542b\u91cf(http:\/\/www.biocloudservice.com\/107\/107.php)\u7b49\u90fd\u53ef\u4ee5\u7528\u672c\u516c\u53f8\u65b0\u5f00\u53d1\u7684\u96f6\u4ee3\u7801\u4e91\u5e73\u53f0\u751f\u4fe1\u5206\u6790\u5c0f\u5de5\u5177\uff0c\u4e00\u952e\u5b8c\u6210\u8be5\u5206\u6790\u5965\uff0c\u611f\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u6b22\u8fce\u6765\u5c1d\u8bd5\u5965\uff0c\u7f51\u5740\uff1ahttp:\/\/www.biocloudservice.com\/home.html\u3002<\/span><span style=\"mso-spacerun:"yes";font-family:\u5fae\u8f6f\u96c5\u9ed1;font-size:10.5000pt;mso-font-kerning:1.0000pt;\">\u4eca\u5929\u5c0f\u679c\u7684\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\uff0c\u4e0b\u671f\u5728\u89c1\u5965\u3002<\/span><\/p>\n<p style=\"text-align: center;\"><br \/><\/p>\n<p><span style=\"mso-spacerun:"yes";font-family:\u5fae\u8f6f\u96c5\u9ed1;font-size:10.5000pt;mso-font-kerning:1.0000pt;\"><\/span><\/p>\n<p><span style=\"mso-spacerun:"yes";font-family:\u5fae\u8f6f\u96c5\u9ed1;font-size:10.5000pt;mso-font-kerning:1.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<section style=\"margin-bottom: 0px;letter-spacing: 0.578px;white-space: normal;caret-color: rgba(0, 0, 0, 0);font-size: 16px;\">\n<section>\n<section style=\"margin-top: 0.5em;\">\n<section style=\"padding: 0.5em;border-width: 1px;border-style: solid;box-shadow: rgb(226, 226, 226) 0px 16px 1px -13px;border-color: rgb(0, 150, 136);\">\n<section style=\"text-align: left;\">\n<section style=\"color: rgb(255, 129, 36);text-align: justify;\">\n<section style=\"margin-bottom: 8px;\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\">\u70b9\u51fb<strong><span style=\"color: rgb(0, 150, 136);\">\u201c\u9605\u8bfb\u539f\u6587\u201d<\/span><\/strong>\u7acb\u523b\u62e5\u6709<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin-bottom: 8px;font-size: 32px;color: rgb(0, 150, 136);\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\">\u2193\u2193\u2193 <\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"display: none;\"><mp-style-type data-value=\"3\"><\/mp-style-type><\/p>\n<div class=\"msg_source_url\"><a href=\"https:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247490130&idx=1&sn=1578a7fab283ba24e1ce5cd6087e2d0d&chksm=cf7c8a97f80b038111f1d3df359dbee67a49462b61b5bfed1060dd83c5d7b975f0db40f4626a#rd\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<p><\/content><\/p>\n<div class=\"msg_source_url\"><a href=\"https:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247490130&idx=1&sn=1578a7fab283ba24e1ce5cd6087e2d0d&chksm=cf7c8a97f80b038111f1d3df359dbee67a49462b61b5bfed1060dd83c5d7b975f0db40f4626a#rd\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<\/div>\n<p><\/body><br \/>\n<\/html><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u642d\u5efa\u751f\u4fe1\u5206\u6790\u6d41\u6c34\u7ebf\uff0c\u5982\u5de5\u5382\u4e00\u683724\u5c0f\u65f6\u8fd0\u8f6cSnakemake\u2014\u2014\u8fdb\u9636\u547d\u4ee4 \u539f\u521b  \u5c0f\u679c&n […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/56018"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=56018"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/56018\/revisions"}],"predecessor-version":[{"id":56021,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/56018\/revisions\/56021"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=56018"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=56018"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=56018"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}