1000 Genome Project 1000 Genome Project 的目标是发现在人群中频率大于1%的变异位点,对来自不同人群的大量样本进行测序,识别到了许多的变异位点,为人类遗传变异的研究提供了一个综合的资源。 整个项目划分为四个阶段,试点阶段和三个主要阶段,主要阶段中只有第一阶段和第三阶段产生了数据,每个阶段数据的详细情况如下...
1.下载1000genome的数据并转为plink格式 下载地址: 在linux中可以使用 wget -c 进行下载 在下载的文件中ALL.panel里包含了人种信息,在本文中没有使用 需要下载的文件 1.1转换为plink格式 注:因为我并不研究x、y染色体,所以并没有做,需要研究的话在循环中加上就好了 for chr in {1..22} do plink -vcf "A...
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Genome Analysis Toolkit vcf: Variant call format DSB: Double strand break CV: Coefficient of variation.References Lander ES: Initial impact of the sequencing of the human genome. Nature. 2011, 470 (7333): 187-197. 10.1038/nature09792. Article CAS PubMed Google Scholar Quail MA, Kozarewa...
VCF files can also be divided by sample name or population using the data slicer. One can view 1000 Genomes data in the context of extensive genome annotation, such as protein-coding genes and whole-genome regulatory information though the dedicated 1000 Genomes browser based on the Ensembl ...
Human reference genome and whole-genome sequences of 2504 individuals in the 1000G project were analyzed in this work. We collected the phase 3 data of 1000G given in variant call format (VCF), which contain haplotype variant information based on the reference genome. VCF files with integrated...
short and long-range LD structure from the genome as well as recombination hotspots. To enable higher computational efficiency, large pools of haplotypes are computed in batches. Each time a VCF file is read, a pool of 1000 haplotypes is automatically generated. Once this pool is exhausted, ano...
This step ensures that the simulated variants data capture both the allele frequency distribution, short and long-range LD structure from the genome as well as recombination hotspots. To enable higher computational efficiency, large pools of haplotypes are computed in batches. Each time a VCF file ...
tabix -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr6.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz 6:7580958-7580959 也可下载比对文件(bam/cram) ---
http://www.internationalgenome.org/data-portal/sample 筛选比对到hg19(GRCh37)的高深度测序的中国样本(不包含傣族)使用的关键词:CHB, CHS, Phase 3, High cov WGS。有86个样本符合要求,点击Download the list下载得到样本名称。 下载在指定区域的SNP基因型信息 ...