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

¹Section for Computational and RNA Biology, University of Copenhagen, Copenhagen 2200, Denmark.

Bioinformatics (Oxford, England)

|January 26, 2024

Summary

This summary is machine-generated.

vcfpp is a new C++ API for fast and safe manipulation of Variant Call Format (VCF/BCF) files. It also enables high-performance R package development for rapid variant analysis.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

The Variant Call Format (VCF/BCF) is widely used for storing genomic variation data.
Increasing big data in genomics necessitates efficient data manipulation tools.
Existing methods may lack speed, flexibility, or cross-language compatibility.

Purpose of the Study:

To develop a fast, flexible, and portable C++ API for VCF/BCF manipulation.
To create a high-performance R package leveraging the C++ API for variant analysis.

Main Methods:

Developed vcfpp, a single-file C++ API for HTSlib.
Implemented an intuitive interface for rapid and safe VCF/BCF file handling.
Created the vcfppR package in R to showcase vcfpp's capabilities.

Main Results:

vcfpp provides an efficient and safe C++ interface for VCF/BCF files.
vcfppR enables high-performance variant analyses within the R environment.
The developed tools are portable across various programming languages.

Conclusions:

vcfpp offers a robust solution for handling large-scale genomic data.
vcfppR facilitates streamlined and accelerated variant analysis workflows.
These tools address the growing demand for efficient bioinformatics data processing.