Changes between Initial Version and Version 1 of WorkPlan


Ignore:
Timestamp:
Sep 12, 2010 11:35:47 PM (14 years ago)
Author:
Morris Swertz
Comment:

--

Legend:

Unmodified
Added
Removed
Modified
  • WorkPlan

    v1 v1  
     1[[TOC()]]
     2= Work plan for quality control, call improvement and phasing (VCF to haplotypes) =
     3
     4Compiled: Yurii Aulchenko, September 12, 2010
     5
     6As noted by Morris, we have to run our project in two phases; phase 1 (from now till the end of 2010) running with minimal personnel (available at present) and phase 2 (starting ~Jan 2011) based on proper resource plan. It is assumed that pilot VCF data will be available at the end of September; we expect all data be available by the January 2011.
     7
     8This document aims to provide an overview of the “VCF to haplotypes” work package.
     9
     10== Plan for phase 1. ==
     11
     12Starting with the end September, when pilot data are available, it is required to build a pipeline for basic post-VCF quality control. This will include two independent sub-projects which may be ran in parallel:
     13
     14'''Chip QC project: '''Crosscheck of the results obtained from BGI with already available GWA scans data.
     15
     16This work package ''aims to'':
     17
     18 * Establish custom pipeline for Chip-based QC.
     19 * Check quality of sequence data.
     20 * Identify factors affecting quality of sequencing (e.g. batch effects).
     21 * Establish (preliminary) thresholds of quality metrics maximizing sensitivity and specificity.
     22 * 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).
     23 * Check if these rates are in agreement with theoretically expected (thus we do not miss any important experimental factor).
     24
     25''Detailedworkflow'' is summarized in a separate document.
     26
     27 * Estimated costs'' for pilot data check and establishing the pipeline:
     28 * 3 months of BI/data manager/programmer at 1.0 fte + experienced supervisor at 0.1 fte.
     29 * Suggested timeline:'' end of September – end of December
     30 * Depends on:'' availability of VCF pilot data
     31 * Other projects depending on this: MendelianQcPipeline (soft), QC’ed data (hard)