PRISM: Pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants

Bioinformatics

Volumn 28, Issue 20, 2012, Pages 2576-2583

  Jiang, Yue ^a,b   Wang, Yadong ^a   Brudno, Michael ^b,c  

^a HARBIN INSTITUTE OF TECHNOLOGY   (China)

^b UNIVERSITY OF TORONTO   (Canada)

^c HOSPITAL FOR SICK CHILDREN   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ALGORITHM; ARTICLE; BASE PAIRING; CHEMISTRY; CHROMOSOME MAP; EVALUATION; GENE DELETION; GENETIC VARIABILITY; GENOMICS; HIGH THROUGHPUT SEQUENCING; HUMAN; INDEL MUTATION; METHODOLOGY;

ALGORITHMS; BASE PAIRING; CHROMOSOME MAPPING; DNA; GENOMIC STRUCTURAL VARIATION; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INDEL MUTATION; SEQUENCE DELETION;

EID: 84870460670     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts484     Document Type: Article

References (21)

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. Chen, K. et al. (2009) BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat. Methods, 6, 677-681.
3. Emde, A.K., Schulz, M.H., Weese, D., Sun, R., Vingron, M., Kalscheuer, V.M., Haas, S.A. and Reinert, K. (2012) Detecting genomic indel variants with exact breakpoints in single-and paired-end sequencing data using SplazerS. Bioinformatics, 28, 619-627.
4. Fiume, M. et al. (2010) Savant: genome browser for high-throughput sequencing data. Bioinformatics, 26, 1938-1944.
5. Fiume, M. et al. (2012) Savant Genome Browser 2: visualization and analysis for population scale genomics. Nucleic Acids Res., 40, W615-W621.
6. Kidd, J.M. et al. (2008) Mapping and sequencing of structural variation from eight human genomes. Nature, 453, 56-64.
7. Karakoc, E. et al. (2011) Detection of structural variants and indels within exome data. Nat. Methods, 9, 176-178.
8. Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
9. Li, H. et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078-2079.
10. McCarroll, S.A. et al. (2007) Copy-number variation and association studies of human disease. Nat. Genet., 40, 1166-1174.
11. McKernan, KJ. et al. (2009) Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res., 19, 1527-1541.
12. McKenna, A. et al. (2010) The Genome Analysis Toolkit: a map reduce framework for analyzing next-generation DNA sequencing data. Genome Res., 20, 1297-1303.
13. Medvedev, P. et al. (2009) Computational methods for discovering structural variation with next-generation sequencing. Nat. Methods, 6, S13-S20.
14. Medvedev, P. et al. (2010) Detecting copy number variation with mated short reads. Genome Res., 20, 1613-1622.
15. Mills, R.E. et al. (2006) An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res., 16, 1182-1190.
16. Mills, R.E. et al. (2011) Mapping copy number variation by population-scale genome sequencing. Nature, 470, 59-65.
17. Nord, A. et al. (2011) Accurate and exact CNV identification from targeted high-throughput sequence data. BMC Genomics, 12, 184.
18. Wang, J. et al. (2011) CREST maps somatic structural variation in cancer genomes with base-pair resolution. Nat. Methods, 8, 652-654.
19. 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.
20. Zhang, J. et al. (2011) SVseq: an approach for detecting exact breakpoints of deletions with low-coverage sequence data. Bioinformatics, 27, 3228-3234.
21. Zhang, J., Wang, J. and Yufeng, Wu (2012) An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data. BMC Bioinformatics, 13 (Suppl. 6), S6.