Homozygous and heterozygous deletions commonly exist in the human genome. For current structural variation detection tools, it is significant to determine whether a deletion is homozygous or heterozygous. However, the problems of sequencing errors, micro-homologies and micro-insertions prohibit common alignment tools from identifying accurate breakpoint locations, and often result in detecting false structural variations. In this paper, we present a novel deletion detection tool called Sprites2. Comparing with Sprites, Sprites2 makes the following modifications: (1) The distribution of insert size is used in Sprites2, which can identify the type of deletions and improves the accuracy of deletion calls; (2) A precise alignment method based on AGE (one algorithm simultaneously aligning 5' and 3' ends between two sequences) is adopted in Sprites2 to identifying breakpoints, which is helpful to resolve the problems introduced by sequencing errors, micro-homologies and micro-insertions. In order to test and verify the performance of Sprites2, some simulated and real datasets are adopted in our experiments, and Sprites2 is compared with five popular tools. According to the experimental results, we can find that Sprites2 can improve deletion detection performance. Sprites2 can be downloaded from https://github.com/zhangzhen/sprites2.