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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 [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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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 several tools for the analysis of next generation sequence data.  
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We are developing [[Software|software tools]] for the analysis of next generation sequence data.  
  
=== [[Read Mapping]] ===
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These tools include:
  
[[Karma|Karma]] - Our fast short read aligner, which generates [[Mapping Quality Scores]]
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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]]
  
[[Karma-colorspace|Karma-ColorSpace]] - QUICKSTART on mapping color space reads
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These tools and additional tools can be found on the [[Software]] page.
  
[[Examples|Examples]] - Sample command lines with discussion
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We are developing Genome/Sequencing Processing Pipelines for anyone to use: [[GotCloud]]
  
=== Variant Calling ===
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== High Level Tutorials  ==
  
[[glfSingle]] - Variant calling for a single, deeply sequenced individual
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Some high-level tutorials on the analysis of next generation sequence data:
  
[[glfTrio]] - Variant calling for a single, deeply sequenced nuclear family with two parents and one child
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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]]
  
[[glfMultiples]] -- Variant calling for multiple, unrelated individuals
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== Projects  ==
  
=== Variant Annotation ===
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[[NHLBI Informatics Resource|NHLBI Genome Sequencing Project]]
  
[[vcfCodingSnps]] -- Annotate coding variants in a VCF file.
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[[SardiNIA]] - The SardiNIA longitudinal study of aging.  
  
=== Quality Control Utilities ===
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[[EMADS|Exome Meta-analysis of Drinking and Smoking (EMADS)]]
  
[[FastQ Validator]] -- Check that a FASTQ file conforms to specification.
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[http://www.1000genomes.org The 1000 Genomes Project]
[[FastQFile]] -- Read a FASTQ file sequence by sequence. Validating the sequence as it is read.
 
[[BamIdentityCheck]] -- Check that mapped reads are consistent with known genotypes for each individual.
 
 
 
=== [[Links to Sequence Analysis Tools|Other Useful Links]] ===
 
 
 
== Projects  ==
 
  
[[SardiNIA]] - The SardiNIA longitudinal study of aging.
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== Learn Genetics  ==
  
[[1000 Genomes Project Pilot 1 SNP Calling]]
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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.
  
== Learn Genetics ==
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== General Resources  ==
  
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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*[[Computer How-Tos]]
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</div>

Latest revision as of 13:50, 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