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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[[Image:2009.08_Group_Retreat_Photo.jpg|400px|center|Group Photo]]
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<!-- Below are old images from 2009 and 2014 Retreats -->
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<!-- <br> [[Image:Abecasis2015Retreat.JPG|700px|center|Group Photo 2015]] -->
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== Welcome! ==
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<!-- <br> [[Image:Abecasis2014Retreat.JPG|700px|center|Group Photo 2014]] -->
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Welcome to our brand new wiki!
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== Welcome! ==
  
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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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Welcome to our wiki!
  
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For basic instructions, see [http://en.wikipedia.org/wiki/Wikipedia:Tutorial the Wikipedia Tutorial].
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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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== Sequence Analysis Tools ==
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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 several tools for the analysis of next generation sequence data.
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== Sequence Analysis Tools  ==
  
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=== [[Read Mapping]] ===
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We are developing [[Software|software tools]] for the analysis of next generation sequence data.
  
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[[Karma|Karma]] - Our fast short read aligner, which generates [[Mapping Quality Scores]]
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These tools include:
  
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[[Karma-colorspace|Karma-ColorSpace]] - QUICKSTART on mapping color space reads
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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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[[Examples|Examples]] - Sample command lines with discussion
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These tools and additional tools can be found on the [[Software]] page.
  
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=== Variant Calling ===
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We are developing Genome/Sequencing Processing Pipelines for anyone to use: [[GotCloud]]
  
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[[glfSingle]] - Variant calling for a single, deeply sequenced individual
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== High Level Tutorials  ==
  
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[[glfTrio]] - Variant calling for a single, deeply sequenced nuclear family with two parents and one child
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Some high-level tutorials on the analysis of next generation sequence data:
  
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[[glfMultiples]] -- Variant calling for multiple, unrelated individuals
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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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=== Variant Annotation ===
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== Projects  ==
  
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[[vcfCodingSnps]] -- Annotate coding variants in a VCF file.
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[[NHLBI Informatics Resource|NHLBI Genome Sequencing Project]]
  
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=== Quality Control Utilities ===
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[[SardiNIA]] - The SardiNIA longitudinal study of aging.
  
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[[FastQ Validator]] -- Check that a FASTQ file conforms to specification.
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[[EMADS|Exome Meta-analysis of Drinking and Smoking (EMADS)]]
  
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[[BamIdentityCheck]] -- Check that mapped reads are consistent with known genotypes for each individual.
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[http://www.1000genomes.org The 1000 Genomes Project]
  
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== Projects ==
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== Learn Genetics  ==
  
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[[SardiNIA]] - The SardiNIA longitudinal study of aging.
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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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== Learn Genetics ==
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== General Resources  ==
  
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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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*[[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"