STR-realigner: A realignment method for short tandem repeat regions

BMC Genomics

Volumn 17, Issue 1, 2016, Pages

  Kojima, Kaname ^a   Kawai, Yosuke ^a   Misawa, Kazuharu ^a   Mimori, Takahiro ^a   Nagasaki, Masao ^a  

^a TOHOKU UNIVERSITY   (Japan)

Author keywords

Alignment; High throughput sequencing; Short tandem repeat

Indexed keywords

COMPARATIVE EFFECTIVENESS; DATA ANALYSIS; ERROR; GENOME; HIGH THROUGHPUT SEQUENCING; INHERITANCE; INTERMETHOD COMPARISON; PROGENY; PUNISHMENT; SHORT TANDEM REPEAT; ALGORITHM; BIOLOGY; DNA SEQUENCE; GENOMICS; PROCEDURES; REPRODUCIBILITY; SEQUENCE ALIGNMENT; SOFTWARE;

MICROSATELLITE DNA;

ALGORITHMS; COMPUTATIONAL BIOLOGY; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICROSATELLITE REPEATS; REPRODUCIBILITY OF RESULTS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 85000979496     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-016-3294-x     Document Type: Article

References (20)

1. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation dna sequencing data. Nat Genet. 2011; 43:491-8.
2. Kojima K, Nariai N, Mimori T, Takahashi M, Yamaguchi-Kabata Y, Sato Y, Nagasaki M. A statistical variant calling approach from pedigree information and local haplotyping with phase informative reads. Bioinformatics. 2013; 29(22):2835-843.
3. Kojima K, Nariai N, Mimori T, Yamaguchi-Kabata Y, Sato Y, Kawai Y, Nagasaki M. Hapmonster: a statistically unified approach for variant calling and haplotyping based on phase-informative reads. Lect Notes Comput Sci. 2014; 8542:107-18.
4. Li H, Ruan J, Durbin R. Mapping short dna sequencing reads and calling variants using mapping quality scores. Genome Res. 2008; 18(11):1851-1858.
5. 1000 Genomes Project Consortium. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012; 491(7422):56-65.
6. Nagasaki JM, Yasuda KF, et al. Rare variant discovery by deep whole-genome sequencing of 1,070 japanese individuals. Nat Commun. 2015; 6:8018.
7. Mimori T, Nariai N, Kojima K, Takahashi M, Ono A, Sato Y, Yamaguchi-Kabata Y, Kawai Y, Nagasaki M. iSVP: an integrated structural variant calling pipeline from high-throughput sequencing data. BMC Syst Biol. 2013; 7(Suppl 6). (S8).
8. Walker FO. Huntington's disease. Lancet. 2007; 369(9557):2185-28.
9. La Spada AR, Wilson EM, Lubahn DB, Harding AE, Fischbeck KH. Androgen receptor gene mutations in x-linked spinal and bulbar muscular atrophy. Nature. 1991; 352(6330):77-9.
10. Gymrek M, Golan D, Rosset S, Erlich Y. lobstr: A short tandem repeat profiler for personal genomes. Genome Res. 2012; 6:1154-1162.
11. Highnam G, Franck C, Martin A, Stephens C, Puthige A, Mittelman D. Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles. Nucleic Acids Res. 2013; 41(1).
12. Cao MD, Tasker E, Willadsen K, Imelfort M, Vishwanathan S, Sureshkumar S, Balasubramanian S, Boden M. Inferring short tandem repeat variation from paired-end short reads. Nucleic Acids Res.2014;42(3).
13. Kojima K, Kawai Y, Nariai N, Mimori T, Hasegawa T, Nagasaki M. Short tandem repeat number estimation from paired-end reads for multiple individuals by considering coalescent tree. BMC Genomics. 2016; 17(494).
14. Ummat A, Bashir A. Resolving complex tandem repeats with long reads. Bioinformatics. 2014; 30(24):3491-498.
15. Tae H, McMahon KW, Settlage RE. Revister: an automated pipeline to revise misaligned reads to simple tandem repeats. Bioinformatics. 2013; 29(14):1734-1741.
16. Benson G. Tandem repeats finder: a program to analyze dna sequences. Nucleic Acids Res. 1999; 27(2):573-80.
17. Misawa K. Short tandem repeats in the human, cow, mouse, chicken, and lizard genomes are concentrated in the terminal regions of chromosomes. Gene Reports. 2016; 4:280-5.
18. 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. A map of human genome variation from population-scale sequencing. Nature. 2010; 467(7422):1061-1073.
19. Li H. Aligning sequence reads, clone sequences and assembly contigs with bwa-mem. arXiv:130.3997. 2013.
20. Pendleton M, Sebra R, Chun Pang AW, Ummat A, Franzen O, Rausch T, Stutz AM, Stedman W, Anantharaman T, Hastie A, Dai H, Fritz MH, Cao H, Cohain A, Deikus G, Durrett RE, Blanchard SC, Altman R, Chin C, Guo Y, Paxinos EE, Korbel JO, Darnell RB, McCombie WR, Kwok P, Mason CE, Schadt EE, A AB. Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nat Methods. 2015; 12(8):780-6.