TY  - JOUR
A1  - Li, Heng
A1  - Ruan, Jue
A1  - Durbin, Richard
T1  - Mapping short DNA sequencing reads and calling variants using mapping quality scores
Y1  - 2008/11/01 
JF  - Genome Research 
JO  - Genome Research 
DO  - 10.1101/gr.078212.108 
UR  - http://genome.cshlp.org/content/early/2008/09/25/gr.078212.108.abstract 
N2  - New sequencing technologies promise a new era in the use of DNA sequence. However, some of these technologies produce very short reads, typically of a few tens of base pairs, and to use these reads effectively requires new algorithms and software. In particular, there is a major issue in efficiently aligning short reads to a reference genome and handling ambiguity or lack of accuracy in this alignment. Here we introduce the concept of mapping quality, a measure of the confidence that a read actually comes from the position it is aligned to by the mapping algorithm. We describe the software MAQ that can build assemblies by mapping shotgun short reads to a reference genome, using quality scores to derive genotype calls of the consensus sequence of a diploid genome, e.g., from a human sample. MAQ makes full use of mate-pair information and estimates the error probability of each read alignment. Error probabilities are also derived for the final genotype calls, using a Bayesian statistical model that incorporates the mapping qualities, error probabilities from the raw sequence quality scores, sampling of the two haplotypes, and an empirical model for correlated errors at a site. Both read mapping and genotype calling are evaluated on simulated data and real data. MAQ is accurate, efficient, versatile, and user-friendly. It is freely available at http://maq.sourceforge.net. 
ER  -