DELLY: structural variant discovery by integrated paired-end and split-read analysis.
DELLY: structural variant discovery by integrated paired-end and split-read analysis.
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DOI：
10.1093/bioinformatics/bts378
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发表时间：
2012-09-15
期刊：
影响因子：
--
通讯作者：
Korbel JO
中科院分区：
文献类型：
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作者：
Rausch T;Zichner T;Schlattl A;Stütz AM;Benes V;Korbel JO
动机：以高灵敏度和特异性发现基因组结构变异（SV）是表征自然发生的变异和理解个人基因组测序数据中的病理性体细胞重排的基本要求。特别感兴趣的是集成的方法，准确地识别简单和复杂的重排异构测序数据集在单核苷酸分辨率，作为研究SV的形成机制和功能后果的最佳基础。结果如下：我们已经开发了一种SV发现方法，称为DELLY，该方法集成了短插入配对末端，长距离配对和分裂读取比对，以准确地描绘单核苷酸分辨率的基因组重排。DELLY适用于检测拷贝数可变缺失和串联重复事件以及平衡重排，如倒位或相互易位。因此，DELLY能够确定基因组重排的全谱，包括复杂事件。在模拟数据上，DELLY在广泛的测序参数范围内优于其他SV预测方法。在真实的数据上，DELLY可靠地揭示了来自1000个基因组计划和癌症基因组的SV，并且随机选择的缺失位点的验证实验显示出高特异性。联系方式：tobias. embl.de www.korbel.embl.de/software.html
Motivation: The discovery of genomic structural variants (SVs) at high sensitivity and specificity is an essential requirement for characterizing naturally occurring variation and for understanding pathological somatic rearrangements in personal genome sequencing data. Of particular interest are integrated methods that accurately identify simple and complex rearrangements in heterogeneous sequencing datasets at single-nucleotide resolution, as an optimal basis for investigating the formation mechanisms and functional consequences of SVs. Results: We have developed an SV discovery method, called DELLY, that integrates short insert paired-ends, long-range mate-pairs and split-read alignments to accurately delineate genomic rearrangements at single-nucleotide resolution. DELLY is suitable for detecting copy-number variable deletion and tandem duplication events as well as balanced rearrangements such as inversions or reciprocal translocations. DELLY, thus, enables to ascertain the full spectrum of genomic rearrangements, including complex events. On simulated data, DELLY compares favorably to other SV prediction methods across a wide range of sequencing parameters. On real data, DELLY reliably uncovers SVs from the 1000 Genomes Project and cancer genomes, and validation experiments of randomly selected deletion loci show a high specificity. Availability: DELLY is available at www.korbel.embl.de/software.html Contact: tobias.rausch@embl.de
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影响因子：
5.8
作者：
Barnett, Derek W.;Garrison, Erik K.;Marth, Gabor T.
通讯作者：
Marth, Gabor T.
影响因子：
64.8
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通讯作者：
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影响因子：
64.5
作者：
Rausch T;Jones DT;Zapatka M;Stütz AM;Zichner T;Weischenfeldt J;Jäger N;Remke M;Shih D;Northcott PA;Pfaff E;Tica J;Wang Q;Massimi L;Witt H;Bender S;Pleier S;Cin H;Hawkins C;Beck C;von Deimling A;Hans V;Brors B;Eils R;Scheurlen W;Blake J;Benes V;Kulozik AE;Witt O;Martin D;Zhang C;Porat R;Merino DM;Wasserman J;Jabado N;Fontebasso A;Bullinger L;Rücker FG;Döhner K;Döhner H;Koster J;Molenaar JJ;Versteeg R;Kool M;Tabori U;Malkin D;Korshunov A;Taylor MD;Lichter P;Pfister SM;Korbel JO
通讯作者：
Korbel JO
影响因子：
5.8
作者：
Rausch, Tobias;Emde, Anne-Katrin;Reinert, Knut
通讯作者：
Reinert, Knut
影响因子：
64.8
作者：
通讯作者：
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