wiki:DeNovoVariationPipeline

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.

Last modified 10 years ago Last modified on Sep 26, 2010 9:54:37 PM