Efficient SNP-sensitive alignment and database-assisted SNP calling for low coverage samples

Abstract

We have designed and implemented an efficient tool for short read alignment that is sensitive to a given set of SNP. In particular, it returns alignments that permit mismatches at these SNPs. We then make use of it to develop a method for detecting SNPs, which allows user to provide annotated SNPs classified in previous studies and use them to guide the execution. By focusing on alignments covering these SNPs, our method greatly accelerates the detection of SNPs at prescribed loci. The annotated SNPs also help us distinguish sequencing errors from authentic SNP alleles easily. We have compared our method with existing methods on several applications. We found that our method have higher accuracy, especially for samples with low coverage. It is faster and can be about two orders of magnitude faster for some applications. Copyright © 2012 ACM.