vipR: Variant identification in pooled DNA using R

Bioinformatics

Volumn 27, Issue 13, 2011, Pages

  Altmann, Andre ^a   Weber, Peter ^a   Quast, Carina ^a   Rex Haffner, Monika ^a   Binder, Elisabeth B ^a   Müller Myhsok, Bertram ^a  

^a MAX PLANCK INSTITUTE OF PSYCHIATRY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER PROGRAM; GENE FREQUENCY; GENERAL ASPECTS OF DISEASE; GENETIC PREDISPOSITION; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN GENOME; POISSON DISTRIBUTION; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL DISTRIBUTION;

DISEASE; GENE FREQUENCY; GENETIC PREDISPOSITION TO DISEASE; GENOME, HUMAN; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; POISSON DISTRIBUTION; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE; STATISTICAL DISTRIBUTIONS;

EID: 79959460560     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr205     Document Type: Article

References (22)

1. Bansal, V. (2010)Astatistical method for the detection of variants from next-generation resequencing of DNA pools. Bioinformatics, 26, i318-i324.
2. Dalca,A.V. and Brudno,M. (2010) Genome variation discovery with high-throughput sequencing data. Brief. Bioinformatics, 11, 3-14.
3. Dohm,J.C. et al. (2008) Substantial biases in ultra-short read data sets from highthroughput DNA sequencing. Nucleic Acids Res., 36, e105.
4. Druley,T.E. et al. (2009) Quantification of rare allelic variants from pooled genomic DNA. Nat. Methods, 6, 263-265.
5. Durbin,R.M. et al. (2010) A map of human genome variation from population-scale sequencing. Nature, 467, 1061-1073.
6. Erhardt,A. et al. (2010) TMEM132D, a new candidate for anxiety phenotypes: evidence from human and mouse studies. Mol. Psychiatry [Epub ahead f print; doi: 10.1038/mp.2010.41].
7. Koboldt,D.C. et al. (2009) VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics, 25, 2283-285.
8. Li,H. and Durbin,R. (2009) Fast and accurate short read alignment with burrowswheeler transform. Bioinformatics, 25, 1754-1760.
9. Li,H. et al. (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res., 18, 1851-1858.
10. Li,H. et al. (2009) The sequence alignment/map format and samtools. Bioinformatics, 25, 2078-2079.
11. Maher,B. (2008) Personal genomes: the case of the missing heritability. Nature, 456, 18-21.
12. Manolio,T.A. et al. (2009) Finding the missing heritability of complex diseases. Nature, 461, 747-753.
13. Out,A.A. et al. (2009) Deep sequencing to reveal new variants in pooled DNAsamples. Hum. Mutat., 30, 1703-1712.
14. R Development Core Team. (2008) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
15. Shendure,J. and Ji,H. (2008) Next-generation DNA sequencing. Nat. Biotechnol., 26, 1135-1145.
16. Skellam,J. (1946) The frequency distribution of the difference between two Poisson variates belonging to different populations. J. R. Stat. Soc. Ser. A, 09, 296.
17. Stratton,M. (2008) Genome resequencing and genetic variation. Nat. Biotechnol., 26, 65-66.
18. Visscher,P.M. et al. (2008) Heritability in the genomics era-concepts and misconceptions. Nat. Rev. Genet., 9, 255-266.
19. Wang,C. et al. (2007) Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Genome Res., 17, 195-1201.
20. Watson,G. (1995) A Treatise on the Theory of Bessel Functions. Cambridge University Press, Cambridge.
21. Wittwer,C.T. et al. (2003) High-resolution genotyping by amplicon melting analysis using LCGreen. Clin. Chem., 49(6 Pt 1), 853-860.
22. Yi,X. et al. (2010) Sequencing of 50 human exomes reveals adaptation to high altitude. Science, 329, 75-78.