Difference between revisions of "Main Page"

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(Sequence Analysis Tools)
(Sequence Analysis Tools)
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#Variant Annotations using [[VcfCodingSnps]]  
 
#Variant Annotations using [[VcfCodingSnps]]  
 
#Rare Variant Analysis using [[RvTests]]  
 
#Rare Variant Analysis using [[RvTests]]  
 +
#Rare Variant Association Analysis in family samples [[FamRvTest]]
 
#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-analysis of single variant or gene-level associations, including tools for generating summary statistics ([[Rvtests]],[[RAREMETALWORKER]]), annotating summary statistics ([[TabAnno]]), and performing meta-analysis (command line tool [[RAREMETAL]] and R package [[RareMETALS]]).
 
#Meta-analysis of single variant or gene-level associations, including tools for generating summary statistics ([[Rvtests]],[[RAREMETALWORKER]]), annotating summary statistics ([[TabAnno]]), and performing meta-analysis (command line tool [[RAREMETAL]] and R package [[RareMETALS]]).
 +
#Sequencing study design helper [[Rarefy]]
  
 
These tools and additional tools can be found on the [[Software]] page.  
 
These tools and additional tools can be found on the [[Software]] page.  

Revision as of 13:03, 12 September 2013


Abecasis Group Wiki


Group Photo 2013


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. 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, including tools for generating summary statistics (Rvtests,RAREMETALWORKER), annotating summary statistics (TabAnno), and performing meta-analysis (command line tool RAREMETAL and R package RareMETALS).
  9. Sequencing study design helper Rarefy

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

Exome Meta-analysis of Drinking and Smoking (EMADS)

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