Paper Info
Title
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.
Year
DOI
Venue
2012
10.1145/2382936.2382957
BCB
Keywords
Field
DocType
previous study,sequencing error,annotated snps,efficient snp-sensitive alignment,short read alignment,low coverage,low coverage sample,prescribed locus,permit mismatches,database-assisted snp,higher accuracy,efficient tool,authentic snp,database
Data mining,Single-nucleotide polymorphism,Locus (genetics),Geography,SNP
Conference
Citations 
PageRank 
References 
0
0.34
6
Authors
8
Name
Order
Citations
PageRank
Ruibang Luo11139.92
Chang Yu233220.83
Chi-Man Liu3967.06
Tak-Wah Lam41860164.96
Thomas Wong500.34
Siu-Ming Yiu619719.88
Ruiqiang Li776591.23
Hing-Fung Ting8396.74