vcfr: a package to manipulate and visualize variant call format data in R

Molecular Ecology Resources

Volumn 17, Issue 1, 2017, Pages 44-53

  Knaus, Brian J ^a   Grünwald, Niklaus J ^a,b  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b OREGON STATE UNIVERSITY   (United States)

Author keywords

data visualization; high throughput sequencing; quality control; variant call format specification

Indexed keywords

BIOLOGY; BIOSTATISTICS; COMPUTER GRAPHICS; POPULATION GENETICS; PROCEDURES; SOFTWARE;

BIOSTATISTICS; COMPUTATIONAL BIOLOGY; COMPUTER GRAPHICS; GENETICS, POPULATION; SOFTWARE;

EID: 84978250280     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12549     Document Type: Conference Paper

References (34)

1. Auwera GA, Carneiro MO, Hartl C et al. (2013) From fastq data to high-confidence variant calls: the genome analysis toolkit best practices pipeline. Current Protocols in Bioinformatics, 43, 11.10.1–11.11.1033.
2. Broad Institute of Harvard and MIT (2015) Phytophthora infestans sequencing project. Available from: http://www.broadinstitute.org (accessed 2015-10-2).
3. Browning SR, Browning BL (2007) Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. The American Journal of Human Genetics, 81, 1084–1097.
4. Campbell NR, Harmon SA, Narum SR (2015) Genotyping-in-thousands by sequencing (GT-seq): a cost effective SNP genotyping method based on custom amplicon sequencing. Molecular Ecology Resources, 15, 855–867.
5. Cooke DE, Cano LM, Raffaele S et al. (2012) Genome analyses of an aggressive and invasive lineage of the Irish potato famine pathogen. PLoS Pathogens, 8, e1002940.
6. Danecek P, Auton A, Abecasis G et al. (2011) The variant call format and VCFtools. Bioinformatics, 27, 2156–2158.
7. DePristo MA, Banks E, Poplin R et al. (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genetics, 43, 491–498.
8. Donlin MJ (2009) Using the generic genome browser (gbrowse). Current Protocols in Bioinformatics, 17:9.9:9.9.1–9.9.24.
9. Dowle M, Srinivasan A, Short T, Lianoglou S, with contributions from Saporta R, Antonyan E (2015) data.table: Extension of data.frame. Available from: https://cran.r-project.org/web/packages/data.table/index.html (accessed 2015-12-4).
10. Eddelbuettel D, Francois R (2011) Rcpp: Seamless R and C++ integration. Journal of Statistical Software, 40, 1–18.
11. Elshire RJ, Glaubitz JC, Sun Q et al. (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One, 6, e19379.
12. Grünwald NJ, McDonald BA, Milgroom MG (2016) Population genomics of fungal and oomycete pathogens. Annual Review of Phytopathology, in press.
13. Haas BJ, Kamoun S, Zody MC et al. (2009) Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature, 461, 393–398.
14. Jombart T (2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics, 24, 1403–1405.
15. Kamvar ZN, Tabima JF, Grünwald NJ (2014) Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ, 2, e281.
16. Kamvar ZN, Brooks JC, Grünwald NJ (2015) Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality. Frontiers in Genetics, 6, 208.
17. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754–1760.
18. Li H, Handsaker B, Wysoker A et al. (2009) The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078–2079.
19. Lu F, Lipka AE, Glaubitz J et al. (2013) Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol. PLoS Genetics, 9, e1003215.
20. Martin MD, Cappellini E, Samaniego JA et al. (2013) Reconstructing genome evolution in historic samples of the Irish potato famine pathogen. Nature Communications, 4, doi: 10.1038/ncomms3172.
21. McKenna A, Hanna M, Banks E et al. (2010) The genome analysis toolkit: a mapreduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20, 1297–1303.
22. Mersmann O (2015) microbenchmark: Accurate Timing Functions. R package version 1.4-2.1. R Foundation for Statistical Computing, Vienna, Austria.
23. Paradis E (2010) pegas: an R package for population genetics with an integrated–modular approach. Bioinformatics, 26, 419–420.
24. Paradis E, Claude J, Strimmer K (2004) APE: analyses of phylogenetics and evolution in R language. Bioinformatics, 20, 289–290.
25. Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One, 7, e37135.
26. R Core Team (2016) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
27. Robinson JT, Thorvaldsdóttir H, Winckler W et al. (2011) Integrative genomics viewer. Nature Biotechnology, 29, 24–26.
28. Samtools (2016) Hts-specs. Available from: http://samtools.github.io/hts-specs/ (accessed 2016-01-27).
29. Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH (2009) Jbrowse: a next-generation genome browser. Genome Research, 19, 1630–1638.
30. Stein LD, Mungall C, Shu S et al. (2002) The generic genome browser: a building block for a model organism system database. Genome Research, 12, 1599–1610.
31. Thorvaldsdóttir H, Robinson JT, Mesirov JP (2012) Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration. Briefings in Bioinformatics, 14, 178–192.
32. Wickham H (2009) ggplot2: Elegant Graphics for Data Analysis. Springer, New York.
33. Wickham H, Francois R (2015) readr: Read Tabular Data. R package version 0.2.2. R Foundation for Statistical Computing, Vienna, Austria.
34. Yoshida K, Schuenemann VJ, Cano LM et al. (2013) The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine. Elife, 2, e00731.