Improved Indel Detection Algorithm Based on Split-Read and Read-Depth

Abstract

Indel is a molecular biology term for an insertion or deletion of bases in the genome. Lots of researches have demonstrated structural variations including indel are closely related to the disease and health of human. So the detection of indel is very important in the life science. Currently, there is a certain number of structural variation detecting algorithms based on next generation sequencing technology. But some of them are not accurate or too sensitive. In this paper, an improved indel detection algorithm based on split-read and read-depth using dynamic programming has been proposed, which is named IDSD. The IDSD algorithm extracts all the discordant paired-end reads. After clustered, the discordant paired-end reads are mapped to the reference sequence using dynamic programming so as to find out the breakpoints in split reads. Then insertions and deletions could be recognized according to the information of structural variations. Furthermore the read depth is also used to detect more deletion and improve higher confidence in the recognition of deletion. The experiment was taken using IDSD and other algorithms. The results show IDSD algorithm has higher efficiency in detecting indel variations and more practical value.