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.