使用.vcf格式的GWAS数据作为暴露的一大好处是可以将工具变量的信息和强度用一张 曼哈顿图 或圈图表示，可以通过下方的代码绘制曼哈顿图或圈图：

VcfR is an R package intended to allow easy manipulation and visualization of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices from the VCF data for use with typical R functions.

一、vcf 格式介绍. vcf （Variant Call Format）是一种用于存储基因组序列中的变异信息. 一般用在 单核苷酸变异（ SNV ），小片段插入缺失（INDEL）等; 也用于 拷贝数变异（ CNV ）， SV （结构变异）等; SNV：参考基因组在1号染色体7845190为 C，但检测样本在同样位置为 A

2024年4月22日 · vcf文件是存放基因变异信息的一种方式，本文提供一种算法，用于读取vcf文件并转换等位基因展示方法、替换染色体展示格式、以及自动识别非唯一变异并进行修改，用于对变异信息进行整理。这里提供一个算法，批量实现对SNP位点的检测与矫正。

VCF(variant call format)是一种文本文件格式(很可能以压缩的方式存储)。 包含元信息行(##为前缀)，标题行(#为前缀)和数据行，每个数据行都包含基因组中某个位置的信息和每个位置上样本的基因型信息(由制表符分隔的文本字段)。

2022年5月31日 · The VCF format can represent single nucleotide variants, multi-nucleotide variants, insertions and deletions, and simple structural variants called and anchored against a reference genome. Here we present a spectrum of over 125 useful, complimentary free and open source software tools and libraries, we wrote and made available through the ...

2016年6月1日 · Vcfanno annotates variants in a VCF file (the “query” intervals) with information aggregated from the set of intersecting intervals among many different annotation files (the “database” intervals) stored in common genomic formats such as BED, GFF, GTF, VCF, and BAM. It utilizes a “streaming” intersection algorithm that leverages ...

The vcf2maf and maf2maf scripts leave most of that responsibility to Ensembl's VEP, but allows you to override their "canonical" isoforms, or use a custom ExAC VCF for annotation. Though the most useful feature is the extensive support in parsing a wide range of crappy MAF-like or VCF-like formats we've seen out in the wild.

Software to call single-nucleotide polymorphisms or related genetic variants has converged on the variant call format (VCF) as the output format of choice. This has created a need for tools to work with VCF files.

2021年5月23日 · VCF can present single nucleotide variants, multi-nucleotide variants, insertions and deletions, and simple structural variants called against a reference genome. Here we present over 125 useful and much used free and open source software tools and libraries, part of vcflib tools and bio-vcf.