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| − | <div style="font-size:162%; border:none; margin:0; padding:.1em; color:#000;">Abecasis Group Wiki</div> | + | {| style="width:100%; background:#fcfcfc; margin-top:1.2em; border:1px solid #ccc;" |
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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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| + | <!-- Below are old images from 2009 and 2014 Retreats --> | ||
| + | <!-- <br> [[Image:Abecasis2015Retreat.JPG|700px|center|Group Photo 2015]] --> | ||
| + | <!-- <br> [[Image:Abecasis2014Retreat.JPG|700px|center|Group Photo 2014]] --> | ||
| + | <!-- <br> [[Image:2009.08 Group Retreat Photo.jpg|center|400px|Group Photo]]--> | ||
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| + | |||
| + | == Welcome! == | ||
| + | |||
| + | Welcome to our 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. | ||
| + | |||
| + | For basic instructions, see [http://en.wikipedia.org/wiki/Wikipedia:Tutorial the Wikipedia Tutorial]. | ||
| + | |||
| + | == Sequence Analysis Tools == | ||
| − | [[ | + | We are developing [[Software|software tools]] for the analysis of next generation sequence data. |
| − | + | These tools include: | |
| − | + | #Variant Calling with [[GlfSingle]] and [[GlfMultiples]] | |
| + | #Variant Calling and De Novo Mutation Detection in Families with [[Polymutt]] | ||
| + | #Variant Annotations using [[VcfCodingSnps]] | ||
| + | #Rare Variant Analysis using [[RvTests]] | ||
| + | #Rare Variant Association Analysis in family samples [[FamRvTest]] | ||
| + | #Quality control using [[C++ Executable: fastQValidator|FastQValidator]], [[VerifyBamID]], and [[BamValidator]] | ||
| + | #C++ APIs for sequence analsysis using [[C++ Library: libStatGen]] | ||
| + | #Meta-analysis of single variant or gene-level associations [[RAREMETAL-SOFTWARE]] | ||
| + | #Sequencing study design helper [[Rarefy]] | ||
| + | #Local ancestry inference (ancestry painting) using off-targeted sequence data [[SEQMIX]] | ||
| + | #Association Container Toolbox [[EPACTS]] | ||
| + | #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: | |
| − | # | + | #[[Evaluating a Read Mapper on Simulated Data]] |
| − | + | #[[SNP Call Set Properties]] | |
| − | + | #[[Generic Exome Analysis Plan]] | |
| − | |||
| − | # | ||
| − | # | ||
== Projects == | == Projects == | ||
| − | [[SardiNIA]] - The SardiNIA longitudinal study of aging. | + | [[NHLBI Informatics Resource|NHLBI Genome Sequencing Project]] |
| + | |||
| + | [[SardiNIA]] - The SardiNIA longitudinal study of aging. | ||
| − | [[ | + | [[EMADS|Exome Meta-analysis of Drinking and Smoking (EMADS)]] |
| − | + | [http://www.1000genomes.org The 1000 Genomes Project] | |
| − | + | == Learn Genetics == | |
| − | + | Faculty in the group teach in a variety of formal and informal settings. [[Class Notes|Class notes]] and relevant discussion are archived here. | |
| − | + | == General Resources == | |
| − | |||
| − | [[ | + | *[[Computer How-Tos]] |
| + | </div> | ||
Latest revision as of 16:06, 23 March 2023
Abecasis Group Wiki
|
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:
- Variant Calling with GlfSingle and GlfMultiples
- Variant Calling and De Novo Mutation Detection in Families with Polymutt
- Variant Annotations using VcfCodingSnps
- Rare Variant Analysis using RvTests
- Rare Variant Association Analysis in family samples FamRvTest
- Quality control using FastQValidator, VerifyBamID, and BamValidator
- C++ APIs for sequence analsysis using C++ Library: libStatGen
- Meta-analysis of single variant or gene-level associations RAREMETAL-SOFTWARE
- Sequencing study design helper Rarefy
- Local ancestry inference (ancestry painting) using off-targeted sequence data SEQMIX
- Association Container Toolbox EPACTS
- 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:
Projects
NHLBI Genome Sequencing Project
SardiNIA - The SardiNIA longitudinal study of aging.
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.
