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

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

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

Workflow

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