2025年2月11日 · The License Calculator for VCF, VVF and vSAN allows users to enter in sample configuration data to run different simulations to determine the subscription licenses required for VCF, VVF and vSAN. Before using the calculator, refer to KB 313548 to learn about the licensing details for VCF, VVF and vSAN.

There are a couple of tools that can plot some statistics of VCF files, including bcftools and jvarkit. However, none of them could: plot specific metrics; customize the plots; focus on variants with certain filters; R package vcfR can do some of the above. However, it has to load entire VCF into memory, which is not friendly to large VCF files.

VCF-kit is a command-line based collection of utilities for performing analysis on Variant Call Format (VCF) files. A summary of the commands is provided below. Obtain frequency/count of genotypes and alleles. Compare variants identified from sequences obtained through alternative methods against a VCF.

vcflib provides methods to manipulate and interpret sequence variation described by VCF. It is both: vclib is both a library (with an API) and a collection of useful tools. The API provides a quick and extremely permissive method to read and write VCF files.

VCF-kit is a collection of utility tools for processing and analyzing the VCF (variant call format) files, including primer generation for variant validation, dendrogram production,genotype imputation from sequence data in linkage studies, and additional tools to be used by statistical and population geneticists.

2021年3月2日 · vcf2fhir converts VCF variants into a FHIR Genomics Diagnostic Report. Conversion translates each VCF row into a corresponding FHIR-formatted variant in the generated report. In scope are simple variants (SNVs, MNVs, Indels), along with zygosity and phase relationships, for autosomes, sex chromosomes, and mitochondrial DNA.

2024年7月19日 · Given a VCF or BCF (binary version of VCF) file, GSC separates the annotation and genotype data and compresses them with different strategies. Particularly, GSC leverages a hierarchical and block-based compression strategy to compress the genotype data.

VCF-kit. About. The Variant Call Format Kit is a collection of tools useful for performing a variety of analyses and operations on variant data stored using the Variant Call Format. VCF-kit is open source and community contributions are encouraged. VCF-kit is open source and is licensed under the MIT License. We welcome community contributions.

2024年2月5日 · 本文详细介绍了VCF文件在遗传学研究中的重要性，包括其格式、各列含义、以及如何处理大文件问题。 特别关注了VCF文件中的关键列如CHROM,POS,REF,ALT等，并提到了GATK等工具在处理和解读VCF文件中的应用。 做过DNA重测序，群体 遗传 进化，BSA，GWAS等项目的人都会遇到VCF文件，这个文件记录了所有样品基因组中所有位置变异（主要包括SNP和InDel）信息。 后续几乎所有的分析内容都是基于此文件，比如进化树分析 …

2024年12月18日 · VCF文件用于存储基因组序列变异信息。 它能够 记录个体基因组中的单核苷酸多态性（SNPs）、插入和缺失（indels）以及其他结构变异。 VCF文件的应用范围广泛，包括但不限于进化树分析、群体结构分析、 主成分分析 （PCA）、全基因组关联研究（GWAS）、二代测序的肿瘤基因组研究等。 VCF文件的主要结构如下所示： 大体由两部分组成： 注释部分和主体内容部分。 我们以一个虚构的VCF文件来看： 注释部分以 “##” 开头，包含文件格式版本、参考 …