VarSim: A high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications

Bioinformatics

Volumn 31, Issue 9, 2015, Pages 1469-1471

  Mu, John C ^a,b   Mohiyuddin, Marghoob ^b   Li, Jian ^b   Bani Asadi, Narges ^b   Gerstein, Mark B ^c   Abyzov, Alexej ^d   Wong, Wing H ^e   Lam, Hugo Y K ^b  

^a Stanford University   (United States)

^b Bina Technologies Inc   (United States)

^c YALE UNIVERSITY   (United States)

^d MAYO CLINIC   (United States)

^e STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER PROGRAM; COMPUTER SIMULATION; GENETIC VARIABILITY; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; HUMAN; MUTATION; NEOPLASM; PROCEDURES; SEQUENCE ALIGNMENT; VALIDATION STUDY;

COMPUTER SIMULATION; GENETIC VARIATION; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MUTATION; NEOPLASMS; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 84931271931     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu828     Document Type: Article

References (16)

1. Abyzov, A. et al. (2011) Cnvnator: An approach to discover, genotype, and characterize typical and atypical cnvs from family and population genome sequencing. Genome Res., 21, 974-984.
2. Bartenhagen, C. and Dugas, M. (2013) RSVSim: An R/Bioconductor package for the simulation of structural variations. Bioinformatics, 29, 1679-1681.
3. Chen, K. et al. (2009) BreakDancer: An algorithm for high-resolution mapping of genomic structural variation. Nat. Methods, 6, 677-681.
4. Cibulskis, K. et al. (2013) Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat. Biotechnol., 31, 213-219.
5. Forbes, S.A. et al. (2014) COSMIC: exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Res, 43, D805-D811.
6. Garrison, E. and Marth, G. (2012) Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907 [q-bio.GN].
7. Huang, W. et al. (2012) ART: A next-generation sequencing read simulator. Bioinformatics, 28, 593-594.
8. Lam, H.Y.K. et al. (2012) Detecting and annotating genetic variations using the HugeSeq pipeline. Nat. Biotechnol., 30, 226-229.
9. Li, H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv, arXiv:1303.3997 [q-bio.GN].
10. MacDonald, J.R. et al. (2014) The Database of Genomic Variants: A curated collection of structural variation in the human genome. Nucleic Acids Res., 42, D986-D992.
11. McKenna, A. et al. (2010) The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res., 20, 1297-1303.
12. Mills, R.E. et al. (2011) Mapping copy number variation by population-scale genome sequencing. Nature, 470, 59-65.
13. Rozowsky, J. et al. (2011) AlleleSeq: Analysis of allele-specific expression and binding in a network framework. Mol. Syst. Biol., 7, 522.
14. Talwalkar, A. et al. (2014) SMaSH: A benchmarking toolkit for human genome variant calling. Bioinformatics, 30, 2787-2795.
15. Ye, K. et al. (2009) Pindel: A pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics, 25, 2865-2871.
16. Zook, J.M. et al. (2014) Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls. Nat. Biotechnol., 32, 246-251.