Changes between Version 2 and Version 3 of TrioAwarePhasingPipeline
- Timestamp:
- Sep 26, 2010 9:12:22 PM (14 years ago)
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TrioAwarePhasingPipeline
v2 v3 1 = TrioAwarePhasingPipeline = 1 [[TOC()]] 2 2 3 Call improvement and phasing 3 = Trio aware phasing = 4 4 5 This is ''phase 2'' project.5 In this project, we will establish an infrastructure and perform phasing of the sequence data. 6 6 7 '''Background.''' We plan to use phased genotypes from GvNL for further imputations. In this, we need high quality of both genotypes and the phasing. 7 == Summary == 8 8 9 ''' Problems.''' It is well recognized that at 12x there is an essential chance that a heterozygous genotype will not be called (estimated roughly as ~1%). Furthermore, for a given individual a certain proportion of the genome will not be covered well; the genotypes at these regions can not be called or will be called with low quality. The effects of such errors and missing data onto further imputations may be large. Other factor affecting quality of further imputations is quality of phasing.9 '''Status''': under development 10 10 11 ''' Proposed solution.''' All above problems can be address in the same framework. Basically, phasing information provides us with the means to fill in missing genotypes and correct erroneously called ones. For example, if in a person coverage is low at a certain regions, we can use information from the first degree relative to figure out what genotypes are there. Sequencing errors can be detected in very much the same way. Thus, phasing and imputations provide us with an attractive opportunity to minimize sequencing errors and proportion of missing data.11 '''Contributors''': Yurii, TBA, TBA 12 12 13 This work package ''aims to'': 13 '''Timeline''': January 2011 – April 2011 (phased genotypes using already existing solutions) - July 2011 (phased genotypes using own solution) - December 2011 (release of software) 14 14 15 · Improve quality of sequence genotypes data by fixing errors and filling in missing values 15 '''Resources''': !PostDoc at 1.0 fte + BI/programmer at 0.5 fte (ideally, the same as the one on MendelianQcPipeline) + experienced supervisor at 0.1 fte 16 16 17 · Phase the genotypes 17 '''Depends on''': availability of QC'ed VCF data (ChipBasedQcPipeline and MendelianQcPipeline) 18 18 19 '' Detailed workflow'' is summarized in a separate document.19 '''Other projects depending on this''': imputations / ImputationPipeline (hard), population genetics (LD, hard), functional variants / SnpAnnotationPipeline (final catalogue, soft), novel variants discovery (final catalogue, soft). 20 20 21 ''Estimated costs'': 12 months of experienced !PostDoc at 1.0 fte + BI/programmer at 0.5 fte + supervisor at 0.1 fte. 21 == Aims and Deliverables == 22 22 23 ''Suggested timeline:'' January 2011 – April 2011 (phased genotypes using already existing solutions) - July 2011 (phased genotypes using own solution) - December 2011 (release of software) 23 * In concert with developments from MendelianQcPipeline, improve quality of sequence genotypes data by fixing errors and filling in missing values 24 * Phase the genotypes 24 25 25 ''Depends on:'' availability of QC’ed genotypes from phase 1 26 == Idea == 26 27 27 ''Other projects depending on this:'' imputations / ImputationPipeline (hard), population genetics (LD, hard), functional variants / SnpAnnotationPipeline (final catalogue, soft), novel variants discovery (final catalogue, soft).28 A principal idea of what questions should be addressed (without saying how) is summarized in TrioAwarePhasingPipelineIdea. 28 29 29 '''Major deliverables'''30 30 31 * Novel methods and software 32 * Improved genotypes 33 * Phasing information 31 == Workflow == 32 33 Automated workflow (will be) provided in TrioAwarePhasingPipelineWorkflow page.
