Difference between revisions of "Main Page"

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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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| style="width:100%; text-align:center; white-space:nowrap; color:#000;" | <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]]
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<!-- <br> [[Image:Abecasis2015Retreat.JPG|700px|center|Group Photo 2015]] -->
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<!-- <br> [[Image:2009.08 Group Retreat Photo.jpg|center|400px|Group Photo]]-->
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== Welcome!  ==
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Welcome to our 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.
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For basic instructions, see [http://en.wikipedia.org/wiki/Wikipedia:Tutorial the Wikipedia Tutorial].
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== Sequence Analysis Tools  ==
  
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[[Image:2009.08_Group_Retreat_Photo.jpg|400px|center|Group Photo]]
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We are developing [[Software|software tools]] for the analysis of next generation sequence data.
  
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== Welcome! ==
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These tools include:
  
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Welcome to our brand new wiki!
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#Variant Calling with [[GlfSingle]] and [[GlfMultiples]]
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#Variant Calling and De Novo Mutation Detection in Families with [[Polymutt]]
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#Variant Annotations using [[VcfCodingSnps]]
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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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If you would like to contribute, [[Special:UserLogin|log-in]] or [http://csgwiki.sph.umich.edu/index.php?title=Special:UserLogin&type=signup create an account]. We recommend using your e-mail address or Michigan uniqname as your user id.
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These tools and additional tools can be found on the [[Software]] page.  
  
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For basic instructions, see [http://en.wikipedia.org/wiki/Wikipedia:Tutorial the Wikipedia Tutorial].
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We are developing Genome/Sequencing Processing Pipelines for anyone to use: [[GotCloud]]
  
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== Sequence Analysis Tools ==
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== High Level Tutorials  ==
  
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We are developing several tools for the analysis of next generation sequence data.
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Some high-level tutorials on the analysis of next generation sequence data:
  
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=== Read Mapping ===
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#[[Evaluating a Read Mapper on Simulated Data]]
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#[[SNP Call Set Properties]]
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#[[Generic Exome Analysis Plan]]
  
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[[Karma|Karma]] - Our fast short read aligner
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== Projects  ==
  
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[[Karma-colorspace|Karma-ColorSpace]] - QUICKSTART on mapping color space reads
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[[NHLBI Informatics Resource|NHLBI Genome Sequencing Project]]
  
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[[Examples|Examples]] - Sample command lines with discussion
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[[SardiNIA]] - The SardiNIA longitudinal study of aging.
  
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=== Variant Calling ===
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[[EMADS|Exome Meta-analysis of Drinking and Smoking (EMADS)]]
  
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[[glfSingle]] - Variant calling for a single, deeply sequenced individual
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[http://www.1000genomes.org The 1000 Genomes Project]
  
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[[glfTrio]] - Variant calling for a single, deeply sequenced nuclear family with two parents and one child
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== Learn Genetics  ==
  
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[[glfMultiples]] -- Variant calling for multiple, unrelated individuals
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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.
  
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=== Variant Annotation ===
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== General Resources  ==
  
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[[vcfCodingSnps]] -- Annotate coding variants in a VCF file.
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*[[Computer How-Tos]]
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</div>

Latest revision as of 16:06, 23 March 2023

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

Retrieved from "http://genome.sph.umich.edu/w/index.php?title=Main_Page&oldid=16408"