75
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchUpdated the group retreat photo to the 2016 one
<!-- BANNER ACROSS TOP OF PAGE -->
<div id="mf-mainpage">
{| style="width:100%; background:#fcfcfc; margin-top:1.2em; border:1px solid #ccc;" |
<!-- BANNER ACROSS TOP OF PAGE -->
<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;"
|-
| 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>
|}
|}
[[Image:AbecasisRetreat2016.jpg|700px|center|Group Photo 2016]]
[[Image:2009.08_Group_Retreat_Photo.jpg|400px|center|Group Photo]]
<!-- 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]]-->
== Welcome! ==
== Welcome! ==
Welcome to our brand new wiki!
Welcome to our wiki!
If you would like to contribute, [[Special:UserLogin|log-in]] or [http://genome.sph.umich.edu/w/index.php?title=Special:UserLogin&type=signup create an account]. We recommend using your e-mail address or Michigan uniqname as your user id.
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].
For basic instructions, see [http://en.wikipedia.org/wiki/Wikipedia:Tutorial the Wikipedia Tutorial].
== Sequence Analysis Tools ==
== Sequence Analysis Tools ==
We are developing [[Software|software tools]] for the analysis of next generation sequence data.
We are developing [[Software|software tools]] for the analysis of next generation sequence data.
# Variant Calling with [[glfSingle]], [[glfTrio]] and [[glfMultiples]]
These tools include:
# Variant Annotations using [[vcfCodingSnps]]
# Quality control using [[C++ Executable: fastQValidator|FastQValidator]], [[VerifyBamID]], and [[BamValidator]]
#Variant Calling with [[GlfSingle]] and [[GlfMultiples]]
# File Readers using [[C++ Library: libbam|BamFile]] and [[C++ Library: libfqf|FastQFile]]
#Variant Calling and De Novo Mutation Detection in Families with [[Polymutt]]
# File Conversions using [[bam2FastQ]]
#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 ==
== High Level Tutorials ==
Some high-level tutorials on the analysis of next generation sequence data:
Some high-level tutorials on the analysis of next generation sequence data:
# [[Evaluating a Read Mapper on Simulated Data]]
#[[Evaluating a Read Mapper on Simulated Data]]
# [[SNP Call Set Properties]]
#[[SNP Call Set Properties]]
# [[Generic Exome Analysis Plan]]
#[[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)]]
[[1000 Genomes Project Pilot 1 SNP Calling]]
[http://www.1000genomes.org The 1000 Genomes Project]
== Learn Genetics ==
== 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.
Faculty in the group teach in a variety of formal and informal settings. [[Class Notes|Class notes]] and relevant discussion are archived here.
==Abecasis Group Meeting==
== General Resources ==
*[[Computer How-Tos]]
</div>
