LUMPY: A probabilistic framework for structural variant discovery

Genome Biology

Volumn 15, Issue 6, 2014, Pages

  Layer, Ryan M ^a   Chiang, Colby ^a   Quinlan, Aaron R ^a,b   Hall, Ira M ^a  

^a UNIVERSITY OF VIRGINIA   (United States)

^b UNIVERSITY OF VIRGINIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME BREAKAGE; GENE FREQUENCY; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC VARIABILITY; HUMAN; HUMAN GENOME; PROBABILITY; SENSITIVITY ANALYSIS; SIGNAL PROCESSING; STRUCTURAL VARIATION; BIOLOGICAL MODEL; DNA MUTATIONAL ANALYSIS; GENETIC VARIATION; GENETICS; HOMOZYGOTE; NEOPLASM; RECEIVER OPERATING CHARACTERISTIC; STATISTICAL MODEL;

CHROMOSOME BREAKPOINTS; DNA MUTATIONAL ANALYSIS; GENE FREQUENCY; GENETIC VARIATION; GENOME, HUMAN; HOMOZYGOTE; HUMANS; MODELS, GENETIC; MODELS, STATISTICAL; NEOPLASMS; ROC CURVE;

EID: 84912096454     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2014-15-6-r84     Document Type: Article

References (31)

1. Alkan C, Coe BP, Eichler EE: Genome structural variation discovery and genotyping. Nat Rev Genet 2011, 12:363-376.
2. Medvedev P, Stanciu M, Brudno M: Computational methods for discovering structural variation with next-generation sequencing. Nat Methods 2009, 6:S13-S20.
3. Rausch T, Zichner T, Schlattl A, Stutz AM, Benes V, Korbel JO: DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 2012, 28:i333-i339.
4. Sindi SS, Onal S, Peng LC, Wu HT, Raphael BJ: An integrative probabilistic model for identification of structural variation in sequencing data. Genome Biol 2012, 13:R22.
5. Handsaker RE, Korn JM, Nemesh J, McCarroll SA: Discovery and genotyping of genome structural polymorphism by sequencing on a population scale. Nat Genet 2011, 43:269-276.
6. Wang J, Mullighan CG, Easton J, Roberts S, Heatley SL, Ma J, Rusch MC, Chen K, Harris CC, Ding L, Holmfeldt L, Payne-Turner D, Fan X, Wei L, Zhao D, Obenauer JC, Naeve C, Mardis ER, Wilson RK, Downing JR, Zhang J: CREST maps somatic structural variation in cancer genomes with base-pair resolution. Nat Methods 2011, 8:652-654.
7. Medvedev P, Fiume M, Dzamba M, Smith T, Brudno M: Detecting copy number variation with mated short reads. Genome Res 2010, 20:1613-1622.
8. Novoalign. [http://www.novocraft.com]
9. Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 2:1754-1760.
10. Faust GG, Hall IM: YAHA: fast and flexible long-read alignment with optimal breakpoint detection. Bioinformatics 2012, 28:2417-2424.
11. Li H, Durbin R: Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 2010, 26:589-595.
12. Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, et al: Mapping copy number variation by population-scale genome sequencing. Nature 2011, 470:59-65.
13. Abyzov A, Urban AE, Snyder M, Gerstein M: CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res 2011, 21:974-984.
14. 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, 43:491-498.
15. Hormozdiari F, Hajirasouliha I, McPherson A, Eichler EE, Sahinalp SC: Simultaneous structural variation discovery among multiple paired-end sequenced genomes. Genome Res 2011, 21:2203-2212.
16. LUMPY. [https://github.com/arq5x/lumpy-sv]
17. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R: The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25:2078-2079.
18. Ye K, Schulz MH, Long Q, Apweiler R, Ning Z: Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 2009, 25:2865-2871.
19. Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, Wendl MC, Zhang Q, Locke DP, Shi X, Fulton RS, Ley TJ, Wilson RK, Ding L, Mardis ER: BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods 2009, 6:677-681.
20. Quinlan AR, Clark RA, Sokolova S, Leibowitz ML, Zhang Y, Hurles ME, Mell JC, Hall IM: Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. Genome Res 2010, 20:623-635.
21. SVsim. [https://github.com/GregoryFaust/SVsim]
22. WGSIM. [https://github.com/lh3/wgsim]
23. Quinlan AR, Hall IM: BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010, 26:841-842.
24. Long-read Pacific Biosciences sequencing of NA12878. [ftp://ftp-trace.ncbi. nih.gov/1000genomes/ftp/technical/working/20131209_na12878_ pacbio/Schadt/]
25. Long-read Moleculo sequencings of NA12878. [ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/working/20131209_na12878_moleculo/]
26. Li H: Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. [http://arxiv.org/abs/1303.3997]
27. Deep whole genome Illumina paired-end sequence data for the CEPH family. [http://www.ebi.ac.uk/ena/data/view/ERP001775]
28. Regions excluded to do abnormally high coverage. [https://github.com/cc2qe/speedseq/blob/master/annotations/ceph18.b37.lumpy.exclude.2014-01-15.bed]
29. Variants released by the 1000 Genomes Project. [ftp://ftp.1000genomes. ebi.ac.uk/vol1/ftp/release/20110521/ALL.wgs.phase1_release_v3.20101123. snps_indels_sv.sites.vcf.gz]
30. The BEDPE file format specification. [http://bedtools.readthedocs.org/en/latest/content/general-usage.html#bedpe-format]
31. Validated variants from the NA12878 genome. [http://www.nature.com/nature/journal/v470/n7332/extref/nature09708-s5.zip]