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.