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= Protocol for Mendelian-error based QC =

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

== Summary ==

'''Status''': under development

'''Contributors''': Yurii, Lennart, Elisa

'''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.