Detecting Break Points of Insertions and Deletions from Paired-end Short Reads
Kai Ye and Zemin Ning
from: Next-generation Sequencing: Current Technologies and Applications (Edited by: Jianping Xu). Caister Academic Press, U.K. (2014)
There is a strong demand in the genomics community to develop effective algorithms to reliably identify all types of genomic variants. Indel and structure variant detection using next-generation sequencing (NGS) data is difficult, and identification of large and complex structural variations is extremely challenging. When applied to NGS data, split-read methods have recently demonstrated their power both in pinpointing the precise breakpoints and in efficient use of computer memory and time, as compared with the read-depth, read-pair and assembly approaches. Pindel and its recent improvements as well as other split-read approaches are reviewed in this article. As each current method can only capture a subset of variant types with a high degree of confidence, a complete software package is needed in the field in order to integrate all types of signals for identifying all genetic variants of different types and size ranges read more ...