Mutation mapping & identification by WGS
http://Genome.CSHLP.org/content/22/8/1541 SNPtrack server, for uploading reads, does #SNP calls & prioritization
This is a novel method for genetic mapping of mutations.
It accomplishes (1) SNP discovery, (2) mutation localization (including
enumerating allele distribution, assessing recombination breakpoint), and
(3) identifying potential causal variants.
In contrast to previous approaches, this method implemented a HMM model
which does not rely on prior knowledge of SNP variation. The HMM model
predicts the recombination events/breakpoints in increasing distance from
the homozygous SNP sites over whole genome.
Software available: SNPtrack
Leshchiner I, Alexa K, Kelsey P, Adzhubei I, Austin C, Cooney J, Anderson H, King M, Stottmann RW, Ha S, Drummond I, Paw BH, North T, Beier D, Goessling W, Sunyaev S. Mutation mapping and identification by whole genome sequencing. Genome Research (2012) 22: 1541-1548.