Vcfpp: a C++ API for rapid processing of the variant call format.

ABSTRACT:

Motivation

Given the widespread use of the variant call format (VCF/BCF) coupled with continuous surge in big data, there remains a perpetual demand for fast and flexible methods to manipulate these comprehensive formats across various programming languages.

Results

This work presents vcfpp, a C++ API of HTSlib in a single file, providing an intuitive interface to manipulate VCF/BCF files rapidly and safely, in addition to being portable. Moreover, this work introduces the vcfppR package to demonstrate the development of a high-performance R package with vcfpp, allowing for rapid and straightforward variants analyses.

Availability and implementation

vcfpp is available from https://github.com/Zilong-Li/vcfpp under MIT license. vcfppR is available from https://cran.r-pr

SUBMITTER: Li Z 

PROVIDER: S-EPMC10868310 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature