UPS-indel: a Universal Positioning System for Indels

dc.contributor.authorHasan, Mohammad Shabbiren
dc.contributor.authorWu, Xiaoweien
dc.contributor.authorWatson, Layne T.en
dc.contributor.authorLi, Zhiyien
dc.contributor.authorZhang, Liqingen
dc.contributor.departmentComputer Scienceen
dc.date.accessioned2017-12-06T19:47:18Zen
dc.date.available2017-12-06T19:47:18Zen
dc.date.issued2017-10-26en
dc.description.abstractStoring biologically equivalent indels as distinct entries in databases causes data redundancy, and misleads downstream analysis. It is thus desirable to have a unified system for identifying and representing equivalent indels. Moreover, a unified system is also desirable to compare the indel calling results produced by different tools. This paper describes UPS-indel, a utility tool that creates a universal positioning system for indels so that equivalent indels can be uniquely determined by their coordinates in the new system, which also can be used to compare different indel calling results. UPS-indel identifies 15% redundant indels in dbSNP, 29% in COSMIC coding, and 13% in COSMIC noncoding datasets across all human chromosomes, higher than previously reported. Comparing the performance of UPS-indel with existing variant normalization tools vt normalize, BCFtools, and GATK LeftAlignAndTrimVariants shows that UPS-indel is able to identify 456,352 more redundant indels in dbSNP; 2,118 more in COSMIC coding, and 553 more in COSMIC noncoding indel dataset in addition to the ones reported jointly by these tools. Moreover, comparing UPS-indel to state-of-the-art approaches for indel call set comparison demonstrates its clear superiority in finding common indels among call sets. UPS-indel is theoretically proven to find all equivalent indels, and thus exhaustive.en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1038/s41598-017-14400-1en
dc.identifier.urihttp://hdl.handle.net/10919/81068en
dc.identifier.volume7en
dc.language.isoen_USen
dc.publisherNatureen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.titleUPS-indel: a Universal Positioning System for Indelsen
dc.title.serialScientific Reportsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
Files
Original bundle
Now showing 1 - 1 of 1
Loading...
Thumbnail Image
Name:
HasanUPS-Indel2017.pdf
Size:
1.5 MB
Format:
Adobe Portable Document Format
License bundle
Now showing 1 - 1 of 1
Name:
license.txt
Size:
1.5 KB
Format:
Item-specific license agreed upon to submission
Description: