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== Welcome! ==

Welcome to our brand new wiki!  

Welcome to our brand new 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.

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].  

== 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:

These tools include:  

# Variant Calling with [[glfSingle]] and [[glfMultiples]]

#Variant Calling with [[GlfSingle]] and [[GlfMultiples]]  

# Variant Calling and De Novo Mutation Detection in Families with [[Polymutt]]

#Variant Calling and De Novo Mutation Detection in Families with [[Polymutt]]  

# Variant Annotations using [[vcfCodingSnps]]

#Variant Annotations using [[VcfCodingSnps]]  

# Rare Variant Analysis using [[rvTests]]

#Rare Variant Analysis using [[RvTests]]  

# Quality control using [[C++ Executable: fastQValidator|FastQValidator]], [[VerifyBamID]], and [[BamValidator]]

#Quality control using [[C++ Executable: fastQValidator|FastQValidator]], [[VerifyBamID]], and [[BamValidator]]  

# C++ APIs for sequence analsysis using [[C++ Library: libStatGen]]

#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]].

#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.

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

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

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

== High Level Tutorials ==

== 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]]

#[[Evaluating a Read Mapper on Simulated Data]]  

# [[SNP Call Set Properties]]

#[[SNP Call Set Properties]]  

# [[Generic Exome Analysis Plan]]

#[[Generic Exome Analysis Plan]]

== Projects  ==

== Projects  ==

[[SardiNIA]] - The SardiNIA longitudinal study of aging.

[[SardiNIA]] - The SardiNIA longitudinal study of aging.  

 

*[[Computer How-Tos]]

* [[Computer How-Tos]]

==Abecasis Group Meeting==

== 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.