Ensembl Variant Effect Predictor (VEP)
Ensembl Variant Effect Predictor (VEP) VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. Simply input the coordinates of your variants and the nucleotide changes to find out the:
VEP web interface - Ensembl
The web interface allows you to access the key features of the VEP without using the command line. Interactively filter your results to find the data you want. Download your results in multiple data formats, easily share your results with others, and integrate your variation data with the powerful Ensembl web browser.
Variant Effect Predictor Data formats - Ensembl
VEP can produce output in the form of serialised JSON objects using the --json flag. JSON is a serialisation format that can be parsed and processed easily by many packages and programming languages; it is used as the default output format for Ensembl's REST server .
ensembl-vep/VEP 注释软件安装及测试 超简单版（conda vep、百 …
2022年3月17日 · VEP 是一款强大的注释、分析 软件，在我们的变异检测中经常使用其进行SNP、INDEL、CNV和 SV 的注释，同时借助数据库的内容，对变异结果进行过滤。 如此一款强大和功能齐全的软件，其参数必然会非常之多，对于初次接触的人来说，过多的参数非常影响对此软件的理解和使用，甚至耗费大量时间来安装软件。 请注意：笔者下载的是 vep=101.0版本，目的是为了与已有的数据库配套，数据库会在后面详解。 Possible precedence issue with control flow …
Variant Effect Predictor Tutorial - Ensembl
Install VEP. Have you downloaded VEP yet? Use git to clone it: git clone https://github.com/Ensembl/ensembl-vep cd ensembl-vep. VEP uses "cache files" or a remote database to read genomic data. Using cache files gives the best performance - let's set one up using the installer: perl INSTALL.pl Hello!
Annotating genetic variants with the VEP, Demo - Ensembl
We have identified five variants on human chromosome nine, C-> A at 128203516, an A deletion at 128328461, C->A at 128322349, C->G at 128323079 and G->A at 128322917. We will use the Ensembl VEP to determine: Have my variants already been annotated in Ensembl? What genes are affected by my variants? Do any of my variants affect gene regulation?
SNP注释神器——VEP（生信） - CSDN博客
2022年12月27日 · VariantEffectPredictor (VEP)是一款强大的基因组变异分析工具，支持多种变异类型的注释，如SNVs、插入和删除等。 VEP提供丰富的注释信息，包括功能影响、群体频率、预测结果和疾病关联等，并支持自定义数据库和插件。 二代测序发现的变异数量是巨大的，以人类基因组为例，1个人类基因组包含近3500000个 SNV 突变和1000个拷贝数变异，其中约20000-25000个变异是在编码区，10000个位点发生了氨基酸编码改变，仅有50-100个发生了蛋白截 …
The Ensembl Variant Effect Predictor - Genome Biology
2016年6月6日 · The VEP annotates variants using a wide range of reference data, including transcripts, regulatory regions, frequencies from previously observed variants, citations, clinical significance information, and predictions of biophysical consequences of variants.
VEP — 高效的变异注释工具 - 腾讯云
2024年4月11日 · VEP —— 高效的基因变异注释工具，可以快速地确定变异在基因组中的位置、影响的转录本以及变异对蛋白质功能的可能影响，例如导致蛋白质结构的改变或功能丧失。 同时它可以处理多种类型的变异，包括单核苷酸变异（SNVs）、插入删除（indels）、拷贝数变异（CNVs）等。 ./vep --cache -i input.txt -o output.txt. --cache # 让 VEP通过本地缓存来加速注释过程。 --genomes # 选项是为了指示 VEP连接到正确的数据库服务器，这个服务器专门存储非 …
Variant Effect Predictor Download and install - Ensembl
VEP's INSTALL.pl makes it easy to set up your environment for using the VEP. It will download and configure a minimal set of the Ensembl API for use by the VEP, and can also download cache files, FASTA files and plugins. Run the following, and follow any prompts as they appear: