Trio aware phasing

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


Status: under development

Contributors: Yurii, Lennart, 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


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


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

Last modified 13 years ago Last modified on Jun 22, 2011 4:07:32 PM