Changes between Version 2 and Version 3 of MendelianQcPipeline

Timestamp:

Sep 26, 2010 8:29:25 PM (14 years ago)

Author:

Yurii Aulchenko

Comment:

--

MendelianQcPipeline

@@ -1 @@
-= MendelianQcPipeline =
+[[TOC()]]
 
-Check for Mendelian inconsistencies exploiting trio structure of the sample.
+= Protocol for Mendelian-error based QC =
 
-This is ''phase 1'' project
+In this project, we will establish an infrastructure to perform QC of genotypic data generated by BGI using Mendelian errors check.
 
-This work package ''aims to'':
+== Summary ==
+
+'''Status''': under development
+
+'''Contributors''': Yurii, Lennart
+
+'''Timeline''': end Sep 2010 - end Dec 2010
+
+'''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)
+
+'''Depends on''': availability of VCF data, ChipBasedQcPipeline (soft)
+
+'''Other projects depending on this''':  ChipBasedQcPipeline (soft), DeNovoVariationPipeline, all projects which start with QC'ed data (e.g. all WP2 projects)
+
+== Aims and Deliverables ==
+
  * Establish custom pipeline for Mendelian-check QC.
  * Check quality of sequence data.
- * Confirm factors (established in ChipBasedQcPipeline) affecting quality of sequencing'''. '''
+ * Confirm factors (established in ChipBasedQcPipeline) affecting quality of sequencing.
  *  Confirm and possibly fine-tune thresholds of quality metrics established in ChipBasedQcPipeline.
  * Confirm the false-positive and false-negative rates for variants discovered in our study (established in ChipBasedQcPipeline).
- * Explore the potential of improvement of calls by exploiting information from the sequencing of relatives (see TrioAwarePhasingPipeline).
+ * Explore the potential of improvement of calls by exploiting information from the sequencing of relatives (see TrioAwareVariantDiscoveryPipeline, TrioAwarePhasingPipeline).
  * Estimate the potential for ''de-novo'' variant discovery based on phasing information (see DeNovoVariationPipeline)
+ * In accord with ChipBasedQcPipeline, provide QC'ed data 
 
-''Detailed workflow'' is summarized in a separate (protocol) document (link will be made from here when available).
+== Idea ==
 
-''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.
+A principal idea of what questions should be addressed (without saying how) is summarized in MendelianQcPipelineIdea.
 
-''Suggested timeline:'' end of September – end of December
 
-''Depends on:'' availability of VCF pilot data, Chip QC (soft)
+== Workflow ==
 
-''Other projects depending on this:'' QC’ed data (hard)
-
-'''Major deliverables of phase 1'''
-
- * Custom pipeline for Mendelian-error based QC
- * 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
-
-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]"] .
-
+Automated workflow (will be) provided in MendelianQcPipelineWorkflow page.