= De-novo variation pipeline = This pipeline aims to discover and verify the 'de-novo' mutations == Summary == '''Status''': idea '''Contributors''': Yurii, Kai, Morris '''Timeline''': TBE '''Resources''': TBE '''Depends on''': availability of FASTQ (hard) and VCF (soft) data, ChipBasedQcPipeline, MendelianQcPipeline '''Other projects depending on this''': no, this is an end-project == Aims and Deliverables == * Establish custom 'de-novo' discovery pipeline * Identify and verify a number of 'de-novo' mutations * Characterize ... == Idea == Because GvNL will do sequencing at 12x, identification of 'de-novo' variants based on simplistic Mendelian checks (see MendelianQcPipeline) is likely to lead to hundreds of thousands of variant, only few of which are truly 'de-novo'. A couple of ideas which may help solving the problem is listed in DeNovoVariationPipelineIdea. BURNING: need to decide what line to follow and come up with realistic plan and estimate for resources needed! == Workflow == Automated workflow (will be) provided in DeNovoVariationPipelineWorkflow page.