一个批量做LDblock的脚本

docs/2024-05/一个批量做LDblock的脚本.md

@@ -0,0 +1,15 @@
+---
+title: "一个批量做LDblock的脚本"
+date: 2024-05-28T10:56:05Z
+draft: ["false"]
+tags: [
+  "fetched",
+  "育种数据分析之放飞自我"
+]
+categories: ["Acdemic"]
+---
+一个批量做LDblock的脚本 by 育种数据分析之放飞自我
+------
+<div><p data-mpa-powered-by="yiban.io">大家好，我是邓飞。</p><p>今天，有小伙伴在星球询问GWAS分析的显著性位点，如何批量绘制LDblock，之前写过LDblock的安装和使用说明：（<a target="_blank" href="http://mp.weixin.qq.com/s?__biz=MzI0MTIzNjYwNQ==&amp;mid=2247492617&amp;idx=1&amp;sn=4a2331c0e29ec4d26f4823c545549fd8&amp;chksm=e90c0b1bde7b820d56cb9fd9ac69f487699ab21efc46c76deca5f32ec5f1d1a70c1023c6ed0e&amp;scene=21#wechat_redirect" textvalue="LDblock绘制连锁不平衡和单体型图" linktype="text" imgurl="" imgdata="null" data-itemshowtype="0" tab="innerlink" data-linktype="2">LDblock绘制连锁不平衡和单体型图</a>）</p><p><img data-galleryid="" data-imgfileid="100011933" data-ratio="0.4758241758241758" data-s="300,640" data-src="https://mmbiz.qpic.cn/mmbiz_png/XEicwVA08daBEojUyMqUQMWODohic09hKzibVsEjfDLbGnhSDX7oz7gUsvUYbR1aspJ3osT6CYLb0KQ7lJT4ZgibibQ/640?wx_fmt=png&amp;from=appmsg" data-type="png" data-w="910" src="https://mmbiz.qpic.cn/mmbiz_png/XEicwVA08daBEojUyMqUQMWODohic09hKzibVsEjfDLbGnhSDX7oz7gUsvUYbR1aspJ3osT6CYLb0KQ7lJT4ZgibibQ/640?wx_fmt=png&amp;from=appmsg"></p><p>问题有3个核心点：<br></p><p>1，snp文件总是有^M符号，怎么去除</p><p>2，如何批量对显著位点进行LDblock分析</p><p>3，有没有现成代码</p><p>今天就搞定这个问题。<br></p><p><br></p><p>首先，看一下正常LDblock分析的代码：<br></p><p>LDBlockShow -InVCF hebing1.vcf -Region 3:400986543:401186543 -OutPng -SeleVar 1 <span>--OutPut re3</span></p><p><span>有vcf文件，染色体，物理位置区间，结果文件名称。<br></span></p><p><span>来一个脚本：</span></p><p><span><br></span></p><section><ul><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li></ul><pre data-lang="bash"><code><span>$ cat ~/bin/plot_ld_plot_vcf.sh </span></code><code><span><span>#!/bin/bash</span></span></code><code><span><br></span></code><code><span><span>if</span> [ <span>$#</span> != 4 ]</span></code><code><span><span>then</span></span></code><code><span>    <span>echo</span> <span>$0</span> name.vcf chronome_number location 20000; 第一个是vcf或者vcf.gz文件，第二个是染色体位置，第三个是物理位置，第四个是上下游区间</span></code><code><span>    <span>exit</span> 1</span></code><code><span><span>fi</span></span></code><code><span><br></span></code><code><span>vcf=<span>$1</span>;chr=<span>$2</span>;pos=<span>$3</span>;qujian=<span>$4</span></span></code><code><span>st=$(( <span>$pos</span> - <span>$qujian</span>))</span></code><code><span>en=$(( <span>$pos</span> + qujian))</span></code><code><span><br></span></code><code><span>ot=re_<span>${chr}</span>_<span>${pos}</span></span></code><code><span><span>echo</span> <span>$chr</span> <span>$pos</span> <span>$pos</span> &gt;temp.txt</span></code><code><span>~/bin/LDBlockShow -InVCF <span>$vcf</span> -Region <span>${chr}</span>:<span>${st}</span>:<span>${en}</span> -SeleVar 1 -BlockType 2 -NoShowLDist 10000000 -OutPut <span>${ot}</span></span></code><code><span>~/bin/ShowLDSVG -InPreFix <span>${ot}</span> -SpeSNPName temp.txt -OutPut <span>${ot}</span>_a</span></code><code><span><br></span></code></pre></section><p><br></p><p>上面的脚本，给定vcf文件，染色体，物理位置，上下游区间，就会自动分析。<br></p><p>如何批量处理呢？<br></p><p>比如snp.txt文件，如下图所示：</p><section><ul><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li></ul><pre data-lang="properties"><code><span><span>1</span> <span>280719882</span></span></code><code><span><span>7</span> <span>143547413</span></span></code><code><span><span>2</span> <span>141942814</span></span></code><code><span><span>2</span> <span>141942735</span></span></code><code><span><span>1</span> <span>175504926</span></span></code><code><span><span>10</span> <span>33619582</span></span></code><code><span><span>1</span> <span>245136244</span></span></code><code><span><span>10</span> <span>134034686</span></span></code><code><span><span>1</span> <span>54049220</span></span></code><code><span><span>1</span> <span>285273845</span></span></code><code><span><span>5</span> <span>18240536</span></span></code><code><span><span>5</span> <span>83233487</span></span></code><code><span><span>8</span> <span>123272935</span></span></code><code><span><span>6</span> <span>93263605</span></span></code><code><span><span>10</span> <span>144172316</span></span></code><code><span><span>10</span> <span>3598262</span></span></code><code><span><span>8</span> <span>4766593</span></span></code><code><span><span>5</span> <span>200813276</span></span></code><code><span><span>8</span> <span>160536300</span></span></code><code><span><span>1</span> <span>286271514</span></span></code><code><span><br></span></code></pre></section><p><br></p><p>上下游区间是100kb，那么先将每个snp生成一个命令行，然后运行就行了。<br></p><p>awk走起：<br></p><section><ul><li><li></ul><pre data-lang="nginx"><code><span><span>awk</span> <span>'{print "bash plot_ld_block_vcf.sh ../geno/genotype.vcf", <span>$1</span>,<span>$2</span>,100000}'</span> snp.txt &gt;temp.sh</span></code><code><span><br></span></code></pre></section><p><br></p><p>生成的脚本文件：</p><section><ul><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li></ul><pre data-lang="properties"><code><span><span>$</span> <span>cat temp.sh </span></span></code><code><span><span>bash</span> <span>plot_ld_block_vcf.sh ../geno/genotype.vcf 1 280719882 100000</span></span></code><code><span><span>bash</span> <span>plot_ld_block_vcf.sh ../geno/genotype.vcf 7 143547413 100000</span></span></code><code><span><span>bash</span> <span>plot_ld_block_vcf.sh ../geno/genotype.vcf 2 141942814 100000</span></span></code><code><span><span>bash</span> <span>plot_ld_block_vcf.sh ../geno/genotype.vcf 2 141942735 100000</span></span></code><code><span><span>bash</span> <span>plot_ld_block_vcf.sh ../geno/genotype.vcf 1 175504926 100000</span></span></code><code><span><span>bash</span> <span>plot_ld_block_vcf.sh ../geno/genotype.vcf 10 33619582 100000</span></span></code><code><span><span>bash</span> <span>plot_ld_block_vcf.sh ../geno/genotype.vcf 1 245136244 100000</span></span></code><code><span><span>bash</span> <span>plot_ld_block_vcf.sh ../geno/genotype.vcf 10 134034686 100000</span></span></code><code><span><span>bash</span> <span>plot_ld_block_vcf.sh ../geno/genotype.vcf 1 54049220 100000</span></span></code><code><span><span>bash</span> <span>plot_ld_block_vcf.sh ../geno/genotype.vcf 1 285273845 100000</span></span></code><code><span><span>bash</span> <span>plot_ld_block_vcf.sh ../geno/genotype.vcf 5 18240536 100000</span></span></code><code><span><span>bash</span> <span>plot_ld_block_vcf.sh ../geno/genotype.vcf 5 83233487 100000</span></span></code><code><span><span>bash</span> <span>plot_ld_block_vcf.sh ../geno/genotype.vcf 8 123272935 100000</span></span></code><code><span><span>bash</span> <span>plot_ld_block_vcf.sh ../geno/genotype.vcf 6 93263605 100000</span></span></code><code><span><span>bash</span> <span>plot_ld_block_vcf.sh ../geno/genotype.vcf 10 144172316 100000</span></span></code><code><span><span>bash</span> <span>plot_ld_block_vcf.sh ../geno/genotype.vcf 10 3598262 100000</span></span></code><code><span><span>bash</span> <span>plot_ld_block_vcf.sh ../geno/genotype.vcf 8 4766593 100000</span></span></code><code><span><span>bash</span> <span>plot_ld_block_vcf.sh ../geno/genotype.vcf 5 200813276 100000</span></span></code><code><span><span>bash</span> <span>plot_ld_block_vcf.sh ../geno/genotype.vcf 8 160536300 100000</span></span></code><code><span><span>bash</span> <span>plot_ld_block_vcf.sh ../geno/genotype.vcf 1 286271514 100000</span></span></code><code><span><br></span></code></pre></section><p>然后运行temp.sh文件就可以了：</p><section><ul><li></ul><pre data-lang="css"><code><span><span>bash</span> <span>temp</span><span>.sh</span></span></code></pre></section><p>静等结果就可以了。</p><p>666<br></p><p><strong>推荐阅读：</strong><br></p><p><strong><br></strong></p><p><strong><strong><span>想要更好的学习和交流，快来加入</span><a target="_blank" href="http://mp.weixin.qq.com/s?__biz=MzI0MTIzNjYwNQ==&amp;mid=2247491476&amp;idx=1&amp;sn=8512962ea1264b569db4aa8d15b8712f&amp;chksm=e90ff086de7879908a1fa151e81004993a15650bae3f68e4d518a332beb18a130373c492043e&amp;scene=21#wechat_redirect" textvalue="飞哥的知识星球" linktype="text" imgurl="" imgdata="null" data-itemshowtype="0" tab="innerlink" data-linktype="2" hasload="1">飞哥的知识星球</a><span>，这是一个生物统计+数量遗传学+GWAS+GS的社区，在这里你可以向飞哥提问、帮你指定学习计划、跟着飞哥一起做实战项目，冲冲冲。</span><a target="_blank" href="http://mp.weixin.qq.com/s?__biz=MzI0MTIzNjYwNQ==&amp;mid=2247491476&amp;idx=1&amp;sn=8512962ea1264b569db4aa8d15b8712f&amp;chksm=e90ff086de7879908a1fa151e81004993a15650bae3f68e4d518a332beb18a130373c492043e&amp;scene=21#wechat_redirect" textvalue="点击这里加入吧：飞哥的学习圈子" linktype="text" imgurl="" 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hasload="1"><span>书籍及配套代码领取--统计遗传分析导论</span></a></p><p><mp-style-type data-value="3"></mp-style-type></p></div>  
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