Trio aware phasing

In this project, we will establish an infrastructure and perform phasing of the sequence data.

Summary

Status: under development

Contributors: Yurii, TBA, TBA

Timeline: January 2011 – April 2011 (phased genotypes using already existing solutions) - July 2011 (phased genotypes using own solution) - December 2011 (release of software)

Resources: PostDoc at 1.0 fte + BI/programmer at 0.5 fte (ideally, the same as the one on MendelianQcPipeline) + experienced supervisor at 0.1 fte

Depends on: availability of QC'ed VCF data (ChipBasedQcPipeline and MendelianQcPipeline)

Other projects depending on this: imputations / ImputationPipeline (hard), population genetics (LD, hard), functional variants / SnpAnnotationPipeline (final catalogue, soft), novel variants discovery (final catalogue, soft).

Aims and Deliverables

• In concert with developments from MendelianQcPipeline, improve quality of sequence genotypes data by fixing errors and filling in missing values
• Higher-quality, more complete and phased genotypes

Idea

A principal idea of what questions should be addressed (without saying how) is summarized in TrioAwarePhasingPipelineIdea.

Workflow

Automated workflow (will be) provided in TrioAwarePhasingPipelineWorkflow? page.