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

被引：1

作者：

Li, Zilong ^{[1
]}

机构：

[1] Univ Copenhagen, Sect Computat & RNA Biol, DK-2200 Copenhagen, Denmark

来源：

BIOINFORMATICS | 2024年 / 40卷 / 02期

关键词：

GENOTYPE IMPUTATION; SEQUENCE;

D O I：

10.1093/bioinformatics/btae049

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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-project.org/web/packages/vcfppR.

引用

页数：4

共 13 条

[1] HTSlib: C library for reading/writing high-throughput sequencing data [J].

Bonfield, James K. ;

Marshall, John ;

Danecek, Petr ;

Li, Heng ;

Ohan, Valeriu ;

Whitwham, Andrew ;

Keane, Thomas ;

Davies, Robert M. .

GIGASCIENCE, 2021, 10 (02)

[2] High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios [J].

Byrska-Bishop, Marta ;

Evani, Uday S. ;

Zhao, Xuefang ;

Basile, Anna O. ;

Abel, Haley J. ;

Regier, Allison A. ;

Corvelo, Andre ;

Clarke, Wayne E. ;

Musunuri, Rajeeva ;

Nagulapalli, Kshithija ;

Fairley, Susan ;

Runnels, Alexi ;

Winterkorn, Lara ;

Lowy, Ernesto ;

Flicek, Paul ;

Germer, Soren ;

Brand, Harrison ;

Hall, Ira M. ;

Talkowski, Michael E. ;

Narzisi, Giuseppe ;

Zody, Michael C. .

CELL, 2022, 185 (18) :3426-+

[3] The variant call format and VCFtools [J].

Danecek, Petr ;

Auton, Adam ;

Abecasis, Goncalo ;

Albers, Cornelis A. ;

Banks, Eric ;

DePristo, Mark A. ;

Handsaker, Robert E. ;

Lunter, Gerton ;

Marth, Gabor T. ;

Sherry, Stephen T. ;

McVean, Gilean ;

Durbin, Richard .

BIOINFORMATICS, 2011, 27 (15) :2156-2158

[4] Rapid genotype imputation from sequence with reference panels [J].

Davies, Robert W. ;

Kucka, Marek ;

Su, Dingwen ;

Shi, Sinan ;

Flanagan, Maeve ;

Cunniff, Christopher M. ;

Chan, Yingguang Frank ;

Myers, Simon .

NATURE GENETICS, 2021, 53 (07) :1104-+

[5] Rapid genotype imputation from sequence without reference panels [J].

Davies, Robert W. ;

Flint, Jonathan ;

Myers, Simon ;

Mott, Richard .

NATURE GENETICS, 2016, 48 (08) :965-+

[6]

Eddelbuettel D, 2011, J STAT SOFTW, V40, P1

[7] A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar [J].

Garrison, Erik ;

Kronenberg, Zev N. N. ;

Dawson, Eric T. T. ;

Pedersen, Brent S. S. ;

Prins, Pjotr .

PLOS COMPUTATIONAL BIOLOGY, 2022, 18 (05)

[8] VCFR: a package to manipulate and visualize variant call format data in R [J].

Knaus, Brian J. ;

Grunwald, Niklaus J. .

MOLECULAR ECOLOGY RESOURCES, 2017, 17 (01) :44-53

[9] The Sequence Alignment/Map format and SAMtools [J].

Li, Heng ;

Handsaker, Bob ;

Wysoker, Alec ;

Fennell, Tim ;

Ruan, Jue ;

Homer, Nils ;

Marth, Gabor ;

Abecasis, Goncalo ;

Durbin, Richard .

BIOINFORMATICS, 2009, 25 (16) :2078-2079

[10] hts-nim: scripting high-performance genomic analyses [J].

Pedersen, Brent S. ;

Quinlan, Aaron R. .

BIOINFORMATICS, 2018, 34 (19) :3387-3389

← 1 2 →