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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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[[Image:AbecasisRetreat2016.jpg|700px|center|Group Photo 2016]]
  
[[Image:2009.08_Group_Retreat_Photo.jpg|400px|center|Group Photo]]
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== Welcome! ==
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== Welcome! ==
  
Welcome to our brand new wiki!
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Welcome to our wiki!  
  
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.
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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.  
  
For basic instructions, see [http://en.wikipedia.org/wiki/Wikipedia:Tutorial the Wikipedia Tutorial].
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For basic instructions, see [http://en.wikipedia.org/wiki/Wikipedia:Tutorial the Wikipedia Tutorial].  
  
== Sequence Analysis Tools ==
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== 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.  
  
# Variant Calling with [[glfSingle]], [[glfTrio]] and [[glfMultiples]]
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These tools include:
# Variant Annotations using [[vcfCodingSnps]]
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# Rare Variant Analysis using [[rvTests]]
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#Variant Calling with [[GlfSingle]] and [[GlfMultiples]]  
# Quality control using [[C++ Executable: fastQValidator|FastQValidator]], [[VerifyBamID]], and [[BamValidator]]
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#Variant Calling and De Novo Mutation Detection in Families with [[Polymutt]]  
# File Readers using [[C++ Library: libbam|BamFile]] and [[C++ Library: libfqf|FastQFile]]
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#Variant Annotations using [[VcfCodingSnps]]  
# File Conversions using [[bam2FastQ]]
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#Rare Variant Analysis using [[RvTests]]
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#Rare Variant Association Analysis in family samples [[FamRvTest]]
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#Quality control using [[C++ Executable: fastQValidator|FastQValidator]], [[VerifyBamID]], and [[BamValidator]]  
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#C++ APIs for sequence analsysis using [[C++ Library: libStatGen]]
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#Meta-analysis of single variant or gene-level associations [[RAREMETAL-SOFTWARE]]
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#Sequencing study design helper [[Rarefy]]
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#Local ancestry inference (ancestry painting) using off-targeted sequence data [[SEQMIX]]
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#Association Container Toolbox [[EPACTS]]
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#Fast Genotype Imputation Tool : [[Minimac3]]
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These tools and additional tools can be found on the [[Software]] page.
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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:
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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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[[NHLBI Informatics Resource|NHLBI Genome Sequencing Project]]
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[[SardiNIA]] - The SardiNIA longitudinal study of aging.  
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[[EMADS|Exome Meta-analysis of Drinking and Smoking (EMADS)]]
  
[[1000 Genomes Project Pilot 1 SNP Calling]]
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[http://www.1000genomes.org The 1000 Genomes Project]
  
== Learn Genetics ==
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== Learn Genetics ==
  
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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Faculty in the group teach in a variety of formal and informal settings. [[Class Notes|Class notes]] and relevant discussion are archived here.  
  
==Abecasis Group Meeting==
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== General Resources  ==
  
3:00-4:30 p.m. on Mondays, room 2610, SPH I.
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*[[Computer How-Tos]]
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Latest revision as of 12:50, 31 August 2016

Abecasis Group Wiki
Group Photo 2016


Welcome!

Welcome to our 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. Rare Variant Association Analysis in family samples FamRvTest
  6. Quality control using FastQValidator, VerifyBamID, and BamValidator
  7. C++ APIs for sequence analsysis using C++ Library: libStatGen
  8. Meta-analysis of single variant or gene-level associations RAREMETAL-SOFTWARE
  9. Sequencing study design helper Rarefy
  10. Local ancestry inference (ancestry painting) using off-targeted sequence data SEQMIX
  11. Association Container Toolbox EPACTS
  12. Fast Genotype Imputation Tool : Minimac3

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

NHLBI Genome Sequencing Project

SardiNIA - The SardiNIA longitudinal study of aging.

Exome Meta-analysis of Drinking and Smoking (EMADS)

The 1000 Genomes Project

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