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= Protocol for comparison between sequencing (VCF) and chip data =

'''Status''': under development

'''Contributors''': Yurii

== Summary ==

Aims of application of the protocol:
 * Establish custom pipeline for Chip-based QC.
 * Check quality of sequence data. 
 * Identify factors affecting quality of sequencing (e.g. batch effects). 
 * Establish (preliminary) thresholds of quality metrics maximizing sensitivity and specificity of genotype calling.
 * Using above thresholds, establish the false-positive and false-negative rates for variants discovered in our study (if we do not take trio structure into account). 
 * Check if these rates are in agreement with theoretically expected (thus we do not miss any important experimental factor). 

== Idea ==

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

A number of 'burning' questions need to be addressed before the idea can be considered finished. These include
* What format will be used for/by Chip data (ChipGtDataFormat)? 
* What factors, potentially affecting or indicating the quality of sequencing data (FactorsRelatedToSeqDataQuality), are to be addressed in the QC?

== Workflow ==

Automated workflow (will be) provided in ChipBasedQcPipelineWorkflow page.