Genetic variations underpin the evolution of all living organisms and conversely the occurrence of Mendelian and complex genetic diseases. Through understanding of rate, type and origin of new mutations, interesting features of an organism’s biology can be revealed. Many facets of the characterisation of de novo mutations in domestic dogs have yet to be explored. With the increased accessibility of next generation sequencing, assessing the whole genomes of parent to offspring trios for inherited (germline) mutations has become feasible. We will do this using 100 base paired-end Illumina HiSeq 2000 sequences with an expected genomic coverage of around 7.5 fold. The sequencing reads will be aligned to the most recent canine reference genome (CanFam3) using Burrows-Wheeler Aligner (BWA), SAMtools and the Genome Analysis Toolkit (GATK) in a best practice alignment protocol. After removal of PCR duplicates and local realignment around insertions and deletions we will call variants, undertake quality control of possible sequencing and alignment errors to exclude artifacts, categorize new mutation types for each trio set, phase haplotypes and validate the haplotype calls and mutation observations through polymerase chain reaction in the laboratory.  At this time we are developing the analysis pipeline and refining it by testing various in-house and open source programs while additional samples are being gathered.