Changes between Version 2 and Version 3 of MendelianQcPipeline


Ignore:
Timestamp:
Sep 26, 2010 8:29:25 PM (12 years ago)
Author:
Yurii Aulchenko
Comment:

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  • MendelianQcPipeline

    v2 v3  
    1 = MendelianQcPipeline =
     1[[TOC()]]
    22
    3 Check for Mendelian inconsistencies exploiting trio structure of the sample.
     3= Protocol for Mendelian-error based QC =
    44
    5 This is ''phase 1'' project
     5In this project, we will establish an infrastructure to perform QC of genotypic data generated by BGI using Mendelian errors check.
    66
    7 This work package ''aims to'':
     7== Summary ==
     8
     9'''Status''': under development
     10
     11'''Contributors''': Yurii, Lennart
     12
     13'''Timeline''': end Sep 2010 - end Dec 2010
     14
     15'''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)
     16
     17'''Depends on''': availability of VCF data, ChipBasedQcPipeline (soft)
     18
     19'''Other projects depending on this''':  ChipBasedQcPipeline (soft), DeNovoVariationPipeline, all projects which start with QC'ed data (e.g. all WP2 projects)
     20
     21== Aims and Deliverables ==
     22
    823 * Establish custom pipeline for Mendelian-check QC.
    924 * Check quality of sequence data.
    10  * Confirm factors (established in ChipBasedQcPipeline) affecting quality of sequencing'''. '''
     25 * Confirm factors (established in ChipBasedQcPipeline) affecting quality of sequencing.
    1126 *  Confirm and possibly fine-tune thresholds of quality metrics established in ChipBasedQcPipeline.
    1227 * Confirm the false-positive and false-negative rates for variants discovered in our study (established in ChipBasedQcPipeline).
    13  * Explore the potential of improvement of calls by exploiting information from the sequencing of relatives (see TrioAwarePhasingPipeline).
     28 * Explore the potential of improvement of calls by exploiting information from the sequencing of relatives (see TrioAwareVariantDiscoveryPipeline, TrioAwarePhasingPipeline).
    1429 * Estimate the potential for ''de-novo'' variant discovery based on phasing information (see DeNovoVariationPipeline)
     30 * In accord with ChipBasedQcPipeline, provide QC'ed data
    1531
    16 ''Detailed workflow'' is summarized in a separate (protocol) document (link will be made from here when available).
     32== Idea ==
    1733
    18 ''Estimated costs'' for pilot data check and establishing the pipeline: 3 months of BI/data manager/programmer at 1.0 fte + experienced supervisor at 0.1 fte.
     34A principal idea of what questions should be addressed (without saying how) is summarized in MendelianQcPipelineIdea.
    1935
    20 ''Suggested timeline:'' end of September – end of December
    2136
    22 ''Depends on:'' availability of VCF pilot data, Chip QC (soft)
     37== Workflow ==
    2338
    24 ''Other projects depending on this:'' QC’ed data (hard)
    25 
    26 '''Major deliverables of phase 1'''
    27 
    28  * Custom pipeline for Mendelian-error based QC
    29  * QC’ed sequence data (also depends on ChipBasedQcPipeline); these data will serve as an input for call improvement, phasing, novel variants, population genetics (variants) and functional variants projects
    30 
    31 Note that after completion of phase 1, preliminary phasing can be done using available [ population-based software (e.g. IMPUTE, MACH, BIMBAM), with haplotypes serving as input for imputations project][file:///C:/Users/MORRIS~1/AppData/Local/Temp/QC%20overview%202010.09.10.doc#_msocom_2 "[YA2]"] .
    32 
     39Automated workflow (will be) provided in MendelianQcPipelineWorkflow page.