Protocol for Mendelian-error based QC

In this project, we will establish an infrastructure to perform QC of genotypic data generated by BGI using Mendelian errors check.

Summary

Status: under development

Contributors: Yurii, Lennart, TBA

Timeline: end Sep 2010 - end Dec 2010

Resources: PostDoc at 0.5 fte + BI/data manager/programmer at 0.25 fte (the same as the one on ChipBasedQcPipeline) + experienced supervisor at 0.1 fte (the same as the one on ChipBasedQcPipeline)

Depends on: availability of VCF data, ChipBasedQcPipeline (soft)

Other projects depending on this: ChipBasedQcPipeline (soft), DeNovoVariationPipeline, all projects which start with QC'ed data (e.g. all WP2 projects)

Aims and Deliverables

• Establish custom pipeline for Mendelian-check QC.
• Check quality of sequence data.
• Confirm factors (established in ChipBasedQcPipeline) affecting quality of sequencing.
• Confirm and possibly fine-tune thresholds of quality metrics established in ChipBasedQcPipeline.
• Confirm the false-positive and false-negative rates for variants discovered in our study (established in ChipBasedQcPipeline).
• Explore the potential of improvement of calls by exploiting information from the sequencing of relatives (see TrioAwareVariantDiscoveryPipeline?, TrioAwarePhasingPipeline).
• Estimate the potential for de-novo variant discovery based on phasing information (see DeNovoVariationPipeline)
• In accord with ChipBasedQcPipeline, provide QC'ed data

Idea

The basic idea of what questions should be addressed (without saying how) is summarized in MendelianQcPipelineIdea.

Workflow

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