Anaconda: AN automated pipeline for somatic COpy Number variation Detection and Annotation from tumor exome sequencing data

BMC Bioinformatics

Software

Jianing Gao¹  Asim Ali¹  Qinghua Shi¹  Rongjun Ban¹  Changlin Wan¹  Xiaohua Jiang²  Huan Zhang²  Yuanwei Zhang²  Zhenghua Yu³  Ao Li³  Qiguang Zang³ 

[1] Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, 230027, Hefei, Anhui, China;Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, 230027, Hefei, Anhui, China;Reproductive Medicine Center of Jinghua Hospital, USTC-Shenyang Jinghua Hospital Joint Center of Human Reproduction and Genetics, 110005, Shenyang, Liaoning, China;School of Information Science and Technology, University of Science and Technology of China, 230027, Hefei, China;

关键词: Copy number variation;    Exome sequencing;    Functional analysis;    Cancer;   

DOI  :  10.1186/s12859-017-1833-3

 received in 2017-03-07, accepted in 2017-09-11,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundCopy number variations (CNVs) are the main genetic structural variations in cancer genome. Detecting CNVs in genetic exome region is efficient and cost-effective in identifying cancer associated genes. Many tools had been developed accordingly and yet these tools lack of reliability because of high false negative rate, which is intrinsically caused by genome exonic bias.ResultsTo provide an alternative option, here, we report Anaconda, a comprehensive pipeline that allows flexible integration of multiple CNV-calling methods and systematic annotation of CNVs in analyzing WES data. Just by one command, Anaconda can generate CNV detection result by up to four CNV detecting tools. Associated with comprehensive annotation analysis of genes involved in shared CNV regions, Anaconda is able to deliver a more reliable and useful report in assistance with CNV-associate cancer researches.ConclusionAnaconda package and manual can be freely accessed at http://mcg.ustc.edu.cn/bsc/ANACONDA/.

【 授权许可】

CC BY   
© The Author(s). 2017