ascatNgs：从全基因组测序数据中识别体细胞获得性拷贝数改变
ascatNgs: Identifying Somatically Acquired Copy-Number Alterations from Whole-Genome Sequencing Data.
作者信息
Raine Keiran M, Van Loo Peter, Wedge David C, Jones David, Menzies Andrew, Butler Adam P, Teague Jon W, Tarpey Patrick, Nik-Zainal Serena, Campbell Peter J
机构信息
Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London, United Kingdom.
出版信息
Curr Protoc Bioinformatics. 2016 Dec 8;56:15.9.1-15.9.17. doi: 10.1002/cpbi.17.
Abstract
We have developed ascatNgs to aid researchers in carrying out Allele-Specific Copy number Analysis of Tumours (ASCAT). ASCAT is capable of detecting DNA copy number changes affecting a tumor genome when comparing to a matched normal sample. Additionally, the algorithm estimates the amount of tumor DNA in the sample, known as Aberrant Cell Fraction (ACF). ASCAT itself is an R-package which requires the generation of many file types. Here, we present a suite of tools to help handle this for the user. Our code is available on our GitHub site (https://github.com/cancerit). This unit describes both 'one-shot' execution and approaches more suitable for large-scale compute farms. © 2016 by John Wiley & Sons, Inc.
摘要
我们开发了ascatNgs，以协助研究人员进行肿瘤的等位基因特异性拷贝数分析（ASCAT）。与匹配的正常样本相比，ASCAT能够检测影响肿瘤基因组的DNA拷贝数变化。此外，该算法可估计样本中肿瘤DNA的量，即异常细胞分数（ACF）。ASCAT本身是一个R包，需要生成多种文件类型。在此，我们提供了一套工具来帮助用户处理这些问题。我们的代码可在我们的GitHub网站（https://github.com/cancerit）上获取。本单元介绍了“一次性”执行方法以及更适合大规模计算集群的方法。© 2016约翰威立国际出版公司。
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本文引用的文献
1
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Nature. 2016 Jun 2;534(7605):47-54. doi: 10.1038/nature17676. Epub 2016 May 2.
2
The variant call format and VCFtools.变异调用格式和 VCFtools。
Bioinformatics. 2011 Aug 1;27(15):2156-8. doi: 10.1093/bioinformatics/btr330. Epub 2011 Jun 7.
3
Efficient storage of high throughput DNA sequencing data using reference-based compression.利用基于参考的压缩技术高效存储高通量 DNA 测序数据。
Genome Res. 2011 May;21(5):734-40. doi: 10.1101/gr.114819.110. Epub 2011 Jan 18.
4
Allele-specific copy number analysis of tumors.肿瘤的等位基因特异性拷贝数分析。
Proc Natl Acad Sci U S A. 2010 Sep 28;107(39):16910-5. doi: 10.1073/pnas.1009843107. Epub 2010 Sep 13.
5
A comprehensive catalogue of somatic mutations from a human cancer genome.一个人类癌症基因组中体细胞突变的综合目录。
Nature. 2010 Jan 14;463(7278):191-6. doi: 10.1038/nature08658. Epub 2009 Dec 16.
6
The Sequence Alignment/Map format and SAMtools.序列比对/映射格式和 SAMtools。
Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8.
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Fast and accurate short read alignment with Burrows-Wheeler transform.使用Burrows-Wheeler变换进行快速准确的短读比对。
Bioinformatics. 2009 Jul 15;25(14):1754-60. doi: 10.1093/bioinformatics/btp324. Epub 2009 May 18.
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