Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection

Michiaki Hamada, Edward Wijaya, Martin C. Frith, Kiyoshi Asai. Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection. Bioinformatics, 27(22):3085-3092, 2011. [doi]