Changes between Version 3 and Version 4 of ChipBasedQcPipeline


Ignore:
Timestamp:
Sep 26, 2010 8:04:19 PM (12 years ago)
Author:
Yurii Aulchenko
Comment:

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  • ChipBasedQcPipeline

    v3 v4  
    33= Protocol for comparison between sequencing (VCF) and chip data =
    44
     5== Summary ==
     6
    57'''Status''': under development
    68
    7 '''Contributors''': Yurii
     9'''Contributors''': Yurii, ???
    810
    9 == Summary ==
     11'''Timeline''': end Sep 2010 - end Dec 2010
    1012
    11 Aims of application of the protocol:
     13'''Resources''': BI/data manager/programmer at 1.0 fte + experienced supervisor at 0.1 fte
     14
     15'''Depends on''': availability of VCF data
     16
     17'''Other projects depending on this''':  MendelianQcPipeline (soft), all projects which start with QC'ed data (e.g. all WP2 projects)
     18
     19== Aims and Deliverables ==
     20
    1221 * Establish custom pipeline for Chip-based QC.
     22 * Verify the identity of the DNA samples
    1323 * Check quality of sequence data.
    1424 * Identify factors affecting quality of sequencing (e.g. batch effects).
     
    1626 * 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).
    1727 * Check if these rates are in agreement with theoretically expected (thus we do not miss any important experimental factor).
     28 * In accord with MendelianQcPipeline, provide QC'ed data
    1829
    1930== Idea ==