Vindel: a simple pipeline for checking indel redundancy

Li, Zhiyi; Wu, Xiaowei; He, Bin; Zhang, Liqing

Vindel: a simple pipeline for checking indel redundancy

dc.contributor.author	Li, Zhiyi	en
dc.contributor.author	Wu, Xiaowei	en
dc.contributor.author	He, Bin	en
dc.contributor.author	Zhang, Liqing	en
dc.contributor.department	Computer Science	en
dc.contributor.department	Statistics	en
dc.date.accessioned	2017-02-03T00:02:39Z	en
dc.date.available	2017-02-03T00:02:39Z	en
dc.date.issued	2014-11-19	en
dc.description.abstract	Background With the advance of next generation sequencing (NGS) technologies, a large number of insertion and deletion (indel) variants have been identified in human populations. Despite much research into variant calling, it has been found that a non-negligible proportion of the identified indel variants might be false positives due to sequencing errors, artifacts caused by ambiguous alignments, and annotation errors. Results In this paper, we examine indel redundancy in dbSNP, one of the central databases for indel variants, and develop a standalone computational pipeline, dubbed Vindel, to detect redundant indels. The pipeline first applies indel position information to form candidate redundant groups, then performs indel mutations to the reference genome to generate corresponding indel variant substrings. Finally the indel variant substrings in the same candidate redundant groups are compared in a pairwise fashion to identify redundant indels. We applied our pipeline to check for redundancy in the human indels in dbSNP. Our pipeline identified approximately 8% redundancy in insertion type indels, 12% in deletion type indels, and overall 10% for insertions and deletions combined. These numbers are largely consistent across all human autosomes. We also investigated indel size distribution and adjacent indel distance distribution for a better understanding of the mechanisms generating indel variants. Conclusions Vindel, a simple yet effective computational pipeline, can be used to check whether a set of indels are redundant with respect to those already in the database of interest such as NCBI’s dbSNP. Of the approximately 5.9 million indels we examined, nearly 0.6 million are redundant, revealing a serious limitation in the current indel annotation. Statistics results prove the consistency of the pipeline on indel redundancy detection for all 22 chromosomes. Apart from the standalone Vindel pipeline, the indel redundancy check algorithm is also implemented in the web server http://bioinformatics.cs.vt.edu/zhanglab/indelRedundant.php.	en
dc.description.version	Published version	en
dc.format.extent	? - ? (10) page(s)	en
dc.format.mimetype	application/pdf	en
dc.identifier.citation	BMC Bioinformatics. 2014 Nov 19;15(1):359	en
dc.identifier.doi	https://doi.org/10.1186/s12859-014-0359-1	en
dc.identifier.issn	1471-2105	en
dc.identifier.uri	http://hdl.handle.net/10919/74912	en
dc.identifier.volume	15	en
dc.language.iso	en	en
dc.publisher	Biomed Central	en
dc.relation.uri	http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000347429700001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=930d57c9ac61a043676db62af60056c1	en
dc.rights	Creative Commons Attribution 4.0 International	en
dc.rights.holder	Zhiyi Li et al.; licensee BioMed Central Ltd.	en
dc.rights.uri	http://creativecommons.org/licenses/by/4.0/	en
dc.subject	Biochemical Research Methods	en
dc.subject	Biotechnology & Applied Microbiology	en
dc.subject	Mathematical & Computational Biology	en
dc.subject	Biochemistry & Molecular Biology	en
dc.subject	Indel redundancy	en
dc.subject	Gap opening	en
dc.subject	Gap extension	en
dc.subject	END SHORT READS	en
dc.subject	DELETIONS	en
dc.subject	INTERFERENCE	en
dc.subject	BREAKPOINTS	en
dc.subject	INSERTIONS	en
dc.subject	ALIGNMENT	en
dc.subject	VARIANTS	en
dc.title	Vindel: a simple pipeline for checking indel redundancy	en
dc.title.serial	BMC Bioinformatics	en
dc.type	Article - Refereed	en
dc.type.dcmitype	Text	en
pubs.organisational-group	/Virginia Tech	en
pubs.organisational-group	/Virginia Tech/All T&R Faculty	en
pubs.organisational-group	/Virginia Tech/Engineering	en
pubs.organisational-group	/Virginia Tech/Engineering/COE T&R Faculty	en
pubs.organisational-group	/Virginia Tech/Engineering/Computer Science	en
pubs.organisational-group	/Virginia Tech/Science	en
pubs.organisational-group	/Virginia Tech/Science/COS T&R Faculty	en
pubs.organisational-group	/Virginia Tech/Science/Statistics	en