Version 3 (modified by Yurii Aulchenko, 14 years ago) (diff)

added 'burning questions'

Table of Contents

  1. Summary
  2. Idea
  3. Workflow

Protocol for comparison between sequencing (VCF) and chip data

Status: under development

Contributors: Yurii


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).


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


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