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	<title>生信菜鸟团 &#187; 基因型</title>
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		<title>居然可以下载千人基因组计划的所有数据bam，vcf数据</title>
		<link>http://www.bio-info-trainee.com/1339.html</link>
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		<pubDate>Thu, 14 Jan 2016 11:54:48 +0000</pubDate>
		<dc:creator><![CDATA[ulwvfje]]></dc:creator>
				<category><![CDATA[基础数据库]]></category>
		<category><![CDATA[vcf]]></category>
		<category><![CDATA[千人基因组]]></category>
		<category><![CDATA[基因型]]></category>

		<guid isPermaLink="false">http://www.bio-info-trainee.com/?p=1339</guid>
		<description><![CDATA[它有两个ftp站点存储所有的数据！ ftp://ftp.1000genomes. &#8230; <a href="http://www.bio-info-trainee.com/1339.html">Continue reading <span class="meta-nav">&#8594;</span></a>]]></description>
				<content:encoded><![CDATA[<div>它有两个ftp站点存储所有的数据！</div>
<div><a href="ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/" target="_blank">ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/</a></div>
<div><a href="ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/">ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/</a></div>
<div>直接看最新版的数据，共有NA编号开头的1182个人，HG开头的1768个人！</div>
<div><a href="ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/phase3/data/">ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/phase3/data/</a></div>
<div>也可以按照人种来查看这些数据：<a href="ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/data/">ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/data/</a></div>
<div>每个人的目录下面都有 四个数据文件夹</div>
<div>Oct 01 2014 00:00    Directory alignment</div>
<div>Oct 01 2014 00:00    Directory exome_alignment</div>
<div>Oct 01 2014 00:00    Directory high_coverage_alignment</div>
<div>Oct 01 2014 00:00    Directory sequence_read</div>
<div>这些数据实在是太丰富了！</div>
<div>也可以直接看最新版的vcf文件，记录了这两千多人的所有变异位点信息！</div>
<div>可以直接看到所有的位点，具体到每个人在该位点是否变异！</div>
<div><a href="ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/">ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/</a></div>
<div></div>
<div>不过它的基因型信息是通过MVNcall+SHAPEIT这个程序call出来的，具体原理见：<a href="http://www.ncbi.nlm.nih.gov/pubmed/23093610">http://www.ncbi.nlm.nih.gov/pubmed/23093610</a></div>
<div>而且网站还提供一些教程：<a href="ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/working/">ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/working/</a></div>
<div>
<div>它有两个ftp站点存储所有的数据！</div>
<div><a href="ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/" target="_blank">ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/</a></div>
<div><a href="ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/">ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/</a></div>
<div>直接看最新版的数据，共有NA编号开头的1182个人，HG开头的1768个人！</div>
<div><a href="ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/phase3/data/">ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/phase3/data/</a></div>
<div>也可以按照人种来查看这些数据：<a href="ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/data/">ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/data/</a></div>
<div>每个人的目录下面都有 四个数据文件夹</div>
<div>Oct 01 2014 00:00    Directory alignment</div>
<div>Oct 01 2014 00:00    Directory exome_alignment</div>
<div>Oct 01 2014 00:00    Directory high_coverage_alignment</div>
<div>Oct 01 2014 00:00    Directory sequence_read</div>
<div>这些数据实在是太丰富了！</div>
<div>也可以直接看最新版的vcf文件，记录了这两千多人的所有变异位点信息！</div>
<div>可以直接看到所有的位点，具体到每个人在该位点是否变异！</div>
<div><a href="ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/">ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/</a></div>
<div></div>
<div>不过它的基因型信息是通过MVNcall+SHAPEIT这个程序call出来的，具体原理见：<a href="http://www.ncbi.nlm.nih.gov/pubmed/23093610">http://www.ncbi.nlm.nih.gov/pubmed/23093610</a></div>
<div>而且网站还提供一些教程：<a href="ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/working/">ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/working/</a></div>
<div><a href="http://www.bio-info-trainee.com/wp-content/uploads/2016/01/clipboard4.png"><img class="alignnone size-full wp-image-1341" src="http://www.bio-info-trainee.com/wp-content/uploads/2016/01/clipboard4.png" alt="clipboard" width="346" height="255" /></a></div>
<div>还有Illumina的450K甲基化芯片数据：<a href="ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/hgsv_sv_discovery/working/20151214_450k_methylation/">ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/hgsv_sv_discovery/working/20151214_450k_methylation/</a></div>
<div>还有一个小程序，<a href="ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/technical/browser/vcf_to_ped_converter/version_1.1/">ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/technical/browser/vcf_to_ped_converter/version_1.1/</a></div>
</div>
<div>还有Illumina的450K甲基化芯片数据：<a href="ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/hgsv_sv_discovery/working/20151214_450k_methylation/">ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/hgsv_sv_discovery/working/20151214_450k_methylation/</a></div>
<div>还有一个小程序，<a href="ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/technical/browser/vcf_to_ped_converter/version_1.1/">ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/technical/browser/vcf_to_ped_converter/version_1.1/</a></div>
<p>&nbsp;</p>
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