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<div style="font-size:162%; border:none; margin:0; padding:.1em; color:#000;">Abecasis Group Wiki</div>
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<br> [[Image:2009.08 Group Retreat Photo.jpg|center|400px|Group Photo]]
  
[[Image:2009.08_Group_Retreat_Photo.jpg|400px|center|Group Photo]]
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== Welcome!  ==
  
== Welcome! ==
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Welcome to our brand new wiki!  
  
Welcome to our brand new wiki!
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If you would like to contribute, [[Special:UserLogin|log-in]] or [[Special:RequestAccount|request an account]]. We recommend using your e-mail address or Michigan uniqname as your user id.
  
If you would like to contribute, [[Special:UserLogin|log-in]] or [[Special:RequestAccount|request an account]]. We recommend using your e-mail address or Michigan uniqname as your user id.
+
For basic instructions, see [http://en.wikipedia.org/wiki/Wikipedia:Tutorial the Wikipedia Tutorial].  
  
For basic instructions, see [http://en.wikipedia.org/wiki/Wikipedia:Tutorial the Wikipedia Tutorial].
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== Sequence Analysis Tools ==
 
 
== Sequence Analysis Tools ==
 
  
 
We are developing [[Software|software tools]] for the analysis of next generation sequence data.  
 
We are developing [[Software|software tools]] for the analysis of next generation sequence data.  
  
These tools include:
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These tools include:  
  
# Variant Calling with [[glfSingle]] and [[glfMultiples]]
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#Variant Calling with [[GlfSingle]] and [[GlfMultiples]]  
# Variant Calling and De Novo Mutation Detection in Families with [[Polymutt]]
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#Variant Calling and De Novo Mutation Detection in Families with [[Polymutt]]  
# Variant Annotations using [[vcfCodingSnps]]
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#Variant Annotations using [[VcfCodingSnps]]  
# Rare Variant Analysis using [[rvTests]]
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#Rare Variant Analysis using [[RvTests]]  
# Quality control using [[C++ Executable: fastQValidator|FastQValidator]], [[VerifyBamID]], and [[BamValidator]]
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#Quality control using [[C++ Executable: fastQValidator|FastQValidator]], [[VerifyBamID]], and [[BamValidator]]  
# C++ APIs for sequence analsysis using [[C++ Library: libStatGen]]
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#C++ APIs for sequence analsysis using [[C++ Library: libStatGen]]  
# Meta-analyze single variants or genes, including tools for generating summary statistics [[rvtests]], annotating summary statistics [[TabAnno]], and performing meta-analysis command line tool [[raremetal]] and R package [[RareMETALS]].
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#Meta-analyze single variants or genes, including tools for generating summary statistics ([[Rvtests]]), annotating summary statistics ([[TabAnno]]), and performing meta-analysis (command line tool [[Raremetal]] and R package [[RareMETALS]]).
  
These tools and additional tools can be found on the [[Software]] page.
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These tools and additional tools can be found on the [[Software]] page.  
  
We are developing Genome/Sequencing Processing Pipelines for anyone to use: [[GotCloud]]
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We are developing Genome/Sequencing Processing Pipelines for anyone to use: [[GotCloud]]  
  
== High Level Tutorials ==
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== High Level Tutorials ==
  
Some high-level tutorials on the analysis of next generation sequence data:
+
Some high-level tutorials on the analysis of next generation sequence data:  
  
# [[Evaluating a Read Mapper on Simulated Data]]
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#[[Evaluating a Read Mapper on Simulated Data]]  
# [[SNP Call Set Properties]]
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#[[SNP Call Set Properties]]  
# [[Generic Exome Analysis Plan]]
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#[[Generic Exome Analysis Plan]]
  
 
== Projects  ==
 
== Projects  ==
  
[[SardiNIA]] - The SardiNIA longitudinal study of aging.
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[[SardiNIA]] - The SardiNIA longitudinal study of aging.  
 +
 
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[[1000 Genomes Project Pilot 1 SNP Calling]]
  
[[1000 Genomes Project Pilot 1 SNP Calling]]
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== Learn Genetics  ==
  
== Learn Genetics ==
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Faculty in the group teach in a variety of formal and informal settings. [[Class Notes|Class notes]] and relevant discussion are archived here.
  
Faculty in the group teach in a variety of formal and informal settings. [[Class Notes|Class notes]] and relevant discussion are archived here.
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== General Resources  ==
  
== General Resources ==
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*[[Computer How-Tos]]
* [[Computer How-Tos]]
 
  
==Abecasis Group Meeting==
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== Abecasis Group Meeting ==
  
 
3:00-4:30 p.m. on Mondays, room 2610, SPH I.
 
3:00-4:30 p.m. on Mondays, room 2610, SPH I.

Revision as of 21:35, 31 March 2013


Abecasis Group Wiki

Group Photo

Welcome!

Welcome to our brand new wiki!

If you would like to contribute, log-in or request an account. We recommend using your e-mail address or Michigan uniqname as your user id.

For basic instructions, see the Wikipedia Tutorial.

Sequence Analysis Tools

We are developing software tools for the analysis of next generation sequence data.

These tools include:

  1. Variant Calling with GlfSingle and GlfMultiples
  2. Variant Calling and De Novo Mutation Detection in Families with Polymutt
  3. Variant Annotations using VcfCodingSnps
  4. Rare Variant Analysis using RvTests
  5. Quality control using FastQValidator, VerifyBamID, and BamValidator
  6. C++ APIs for sequence analsysis using C++ Library: libStatGen
  7. Meta-analyze single variants or genes, including tools for generating summary statistics (Rvtests), annotating summary statistics (TabAnno), and performing meta-analysis (command line tool Raremetal and R package RareMETALS).

These tools and additional tools can be found on the Software page.

We are developing Genome/Sequencing Processing Pipelines for anyone to use: GotCloud

High Level Tutorials

Some high-level tutorials on the analysis of next generation sequence data:

  1. Evaluating a Read Mapper on Simulated Data
  2. SNP Call Set Properties
  3. Generic Exome Analysis Plan

Projects

SardiNIA - The SardiNIA longitudinal study of aging.

1000 Genomes Project Pilot 1 SNP Calling

Learn Genetics

Faculty in the group teach in a variety of formal and informal settings. Class notes and relevant discussion are archived here.

General Resources

Abecasis Group Meeting

3:00-4:30 p.m. on Mondays, room 2610, SPH I.