Changes between Version 3 and Version 4 of ChipBasedQcPipeline

Timestamp:

Sep 26, 2010 8:04:19 PM (14 years ago)

Author:

Yurii Aulchenko

Comment:

--

ChipBasedQcPipeline

@@ -3 +3 @@
 = Protocol for comparison between sequencing (VCF) and chip data =
 
+== Summary ==
+
 '''Status''': under development
 
-'''Contributors''': Yurii
+'''Contributors''': Yurii, ???
 
-== Summary ==
+'''Timeline''': end Sep 2010 - end Dec 2010
 
-Aims of application of the protocol:
+'''Resources''': BI/data manager/programmer at 1.0 fte + experienced supervisor at 0.1 fte
+
+'''Depends on''': availability of VCF data
+
+'''Other projects depending on this''':  MendelianQcPipeline (soft), all projects which start with QC'ed data (e.g. all WP2 projects)
+
+== Aims and Deliverables ==
+
  * Establish custom pipeline for Chip-based QC.
+ * Verify the identity of the DNA samples
  * Check quality of sequence data. 
  * Identify factors affecting quality of sequencing (e.g. batch effects). 
@@ -16 +26 @@
  * 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). 
+ * In accord with MendelianQcPipeline, provide QC'ed data 
 
 == Idea ==