<div id="mf-mainpage">


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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]]






== 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 ==

[[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>

File:AbecasisRetreat2016.jpg

2016-08-31T17:47:51Z

Amkwong:

Abecasis Lab

2016-05-13T12:58:21Z

Amkwong: Updated Lars's title

[[Image:Abecasis2015Retreat.JPG|750px|center|Group Photo 2015]]



== Mission Statement ==

We are developing and applying computational and statistical tools to further understanding of complex human diseases, such as cardiovascular disease and diabetes.

== Leadership ==

[[Goncalo Abecasis]] is currently the Felix Moore Collegiate Professor of Biostatistics at the University of Michigan School of Public Health.

== Current Members ==

=== Research Fellows ===

[[File:Kuser.png|50px]] Christian Fuchsberger

[[File:PicJingjing.jpg|50px]] Jingjing Yang

=== Graduate Students ===

[[File:Brieger_Katharine_1.jpg|50px]] Katharine Brieger

[[File:SaiChen.jpg|50px]] Sai Chen

[[File:HeadOfAlanKwong.jpg|50px]] [[Alan Kwong]]

[[File:Kuser.png|50px]] Sebanti Sengupta

[[File:Gregory3.jpg|50px]] Greg Zajac

[[File:Kuser.png|50px]] Fan Zhang

[[File:Wanlin.jpg|50px]] Wanlin Zheng

[[File:Kuser.png|50px]] Wei Zhou

[[File:Xutong.jpg|50px]] Xutong Zhao

=== Staff ===

[[File:Irene_headshot.jpg|50px]] Irene Felicetti : Administrative Assistant Sr.

[[File:TomBlackwell_crop.jpg|50px]] [[Tom Blackwell]] : Research Area Specialist Sr.

[[File:Sean_head.jpg|50px]] [[Sean Caron]] : UNIX Systems Administrator

[[File:Headshot-chris-clark-2 (3).jpg|50px]] Chris Clark : Applications Programmer/Analyst Sr.

[[File:Kuser.png|50px]] Jonathon LeFaive : Applications Programmer/Analyst Sr.

[[File:Kevin_Web-Profile.jpg ‎|50px]] Kevin Li : Web Applications Developer

[[File:Kuser.png|50px]] Ellen Schmidt : Research Area Specialist Lead

[[File:Kuser.png|50px]] Peter VandeHaar : Applications Programmer/Analyst Sr.

[[File:MK_head.jpg|50px]] [[Mary Kate Wing]] : Applications Programmer working on GotCloud Pipelines, C++ library & tools (libStatGen, bamUtils)

== Alumni ==

=== Former Research Faculty ===

* Hyun Min Kang (''graduated in 2011''), now Assistant Professor at the [http://www.sph.umich.edu/biostat/ University of Michigan School of Public Health, Department of Biostatistics].

=== Former Research Fellows ===

* Weimin Chen (graduated 2007), now Associate Professor at the [http://people.virginia.edu/~wc9c/ Department of Public Health Sciences & Center for Public Health Genomics, University of Virginia]

* Goo Jun (graduated 2008), now Assistant Professor at the [https://scholar.google.com/citations?user=1wzhcEQAAAAJ&hl=en University of Texas Health Sciences Center]

* Bingshan Li (graudated 2011), now Assistant Professor at the [https://medschool.vanderbilt.edu/cqs/people/Bingshan/Li/cqs-faculty-members Center for Quantitative Sciences, Vanderbilt University]

* [[Dajiang Liu]] (graduated 2013), now Assistant Professor at the [http://www-personal.umich.edu/~dajiang/ Penn State University College of Medicine]

* Serena Sanna (graduated 2007), now an investigator at the [http://www.serenasanna.com/ Istituto di Neurogenetica e Neurofarmacologia in Sardinia, Italy]

* Paul Scheet (graduated 2008), now Associate Professor at [http://faculty.mdanderson.org/Paul_Scheet/Default.asp?SNID=221605974 Department of Epidemiology, University of Texas MD Anderson Cancer Center]

* Carlo Sidore (graduated 2012), now an investigator at the [http://www.cnr.it/istituti/DatiGenerali.html?cds=060 Istituto di Neurogenetica e Neurofarmacologia in Sardinia, Italy]

* Fabio Busonero (graduated 2012), now an investigator at the [http://www.cnr.it/istituti/DatiGenerali.html?cds=060 Istituto di Neurogenetica e Neurofarmacologia in Sardinia, Italy]

* William Stewart (graduated 2008), now Assistant Professor at [http://www.mathmed.org/#William_Stewart Battelle Center for Computational Medicine, Departments of Statistics and Pediatrics, National Children's Hospital and Ohio State University]

* Alex Tsoi (graduated 2014), now Research Assistant Professor at [https://www.med.umich.edu/DERM/faculty/alextsoi_pub.shtml University of Michigan Medical School]

* [[Scott Vrieze]] (graduated 2014), now an Assistant Professor of Psychology and Neuroscience at [http://www.colorado.edu/ibg/people/471 University of Colorado, Boulder]

* [[Lars Fritsche]] (graduated 2016), now an Associate Professor at [http://www.ntnu.edu/ism the Department of Public Health and General Practice at the Norwegian University of Science and Technology] in Trondheim, Norway

=== Former Doctoral Students ===

* Wei Chen (graduated 2011), now Assistant Professor at the [http://www.chp.edu/CHP/Chen%2C+Wei%2C+PhD Department of Pediatrics, University of Pittsburgh Medical Center]

* Jun Ding (graduated 2010), now Staff Scientist / Facility Head at the [http://www.grc.nia.nih.gov/branches/lg/lg.htm Laboratory of Genetics, National Institute on Aging (NIH)].

* Shuang Feng (graduated 2015), now Research Scientist at Big Data Lab at Hitachi America Ltd.

* Weihua Guan (graduated 2010), now Assistant Professor at the [http://sph.umn.edu/faculty1/expertise/statistical-genetics/name/weihua-guan/ Department of Biostatistics, University of Minnesota School of Public Health].

* Yun Li (graduated 2009), now Assistant Professor at the [http://www.sph.unc.edu/?option=com_profiles&Itemid=6138&profileAction=ProfDetail&pid=708777879 Department of Biostatistics, University of North Carolina].

* Youna Hu (graduated 2012), now a Data Sciences Engineer at A9, a subsidiary of Amazon.com

* Mingyao Li (graduated 2005), now Associate Professor at the [http://www.cceb.upenn.edu/faculty/index.php?id=159 Department of Biostatistics and Epidemiology, University of Pennsylvania]

* Liming Liang (graduated 2009), now Assistant Professor at the [http://www.hsph.harvard.edu/faculty/liming-liang/ Departments of Biostatistics and Epidemiology, Harvard University]

* Tasha Fingerlin (graduated 2003), now Associate Professor at the [http://www.ucdenver.edu/academics/colleges/PublicHealth/departments/Epidemiology/About/Faculty/Pages/FingerlinT.aspx Section of Epidemiology and Community Health, University of Colorado Health Sciences Center]

* Sara Rashkin (graduated 2015), now Post Doc at [http://wittelab.ucsf.edu/pages/people UCSF Witte Lab]

* Andrew Skol (graduated 2006), now Assistant Professor at the [http://med-www02.bsd.uchicago.edu/339/FacultyPro/faculty_profile.aspx?empl_id=10164 Section of Genetic Medicine, University of Chicago]

* [[Xiaowei Zhan]] (graduated 2014), now Assistant Professor at the [http://profiles.utsouthwestern.edu/profile/152189/xiaowei-zhan.html Department of Clinical Science, University of Texas - Southwestern Medical Center].

* Jin Zhen (graduated 2009), now working in the Pharmaceutical Industry.

=== Former Masters Students ===

* Su Chu

* Nate Cohen

* Melinda Curran

* Vesela Gateva

* Xijing Han

* Dan Hovelson

* Elizabeth Jewell

* Michelle Kleckner

* Ben Lerch

* Yanming Li

* Heather Munro

* Nick Seewald

* Theresa Scott (nee Daigneault)

* Matthew Snyder

* Vivian Wang

* Yuan Wei

* Abigail Woodroffe

* Zaojun Ye

* Matthew Zawitowski

* Anita Yu Zhao

* Tingting Zhou

=== Former Staff ===

* Paul Anderson

* Laura Baker

* [[Jennifer Bragg-Gresham]]

* Johanna Forster

* Jan Wigginton

=== Visitors ===

* Qing Lu

* Andrea Maschio

* Giorgio Pistis

* Eleanora Porcu

* Toshiko Tanakato

== Really Useful Stuff ==

* [[Abecasis Group Awards]]
* [https://calendars.office.microsoft.com/pubcalstorage/m3n2kr0z1470909/Goncalo_Abecasis_Calendar(1).ics Goncalo's Calendar]

Abecasis Lab

2016-01-27T18:30:09Z

Amkwong:

[[Image:Abecasis2015Retreat.JPG|750px|center|Group Photo 2015]]



== Mission Statement ==

We are developing and applying computational and statistical tools to further understanding of complex human diseases, such as cardiovascular disease and diabetes.

== Leadership ==

[[Goncalo Abecasis]] is currently the Felix Moore Collegiate Professor of Biostatistics at the University of Michigan School of Public Health.

== Current Members ==

=== Research Fellows ===

[[File:Kuser.png|50px]] Christian Fuchsberger

[[File:LarsFritsche_crop.jpg|50px]] [[Lars Fritsche]]

[[File:PicJingjing.jpg|50px]] Jingjing Yang

=== Graduate Students ===

[[File:Brieger_Katharine_1.jpg|50px]] Katharine Brieger

[[File:Kuser.png|50px]] Sai Chen

[[File:Kuser.png|50px]] Nate Cohen

[[File:SantyPic.jpeg|50px]] [[Sayantan Das|Sayantan Das]]

[[File:Kuser.png|50px]] Michelle Kleckner

[[File:HeadOfAlanKwong.jpg|50px]] [[Alan Kwong]]

[[File:Kuser.png|50px]] Sebanti Sengupta

[[File:Gregory3.jpg|50px]] Greg Zajac

[[File:Kuser.png|50px]] Fan Zhang

[[File:Kuser.png|50px]] Wanlin Zheng

[[File:Kuser.png|50px]] Wei Zhou

[[File:Xutong.jpg|50px]] Xutong Zhou

=== Staff ===

[[File:Irene_headshot.jpg|50px]] Irene Felicetti : Administrative Assistant Sr.

[[File:TomBlackwell_crop.jpg|50px]] [[Tom Blackwell]] : Research Area Specialist Sr.

[[File:Sean_head.jpg|50px]] [[Sean Caron]] : UNIX Systems Administrator

[[File:Headshot-chris-clark-2 (3).jpg|50px]] Chris Clark : Applications Programmer/Analyst Sr.

[[File:Kevin_Web-Profile.jpg ‎|50px]] Kevin Li : Web Applications Developer

[[File:MK_head.jpg|50px]] [[Mary Kate Wing]] : Applications Programmer working on GotCloud Pipelines, C++ library & tools (libStatGen, bamUtils)

[[File:Johanna_Web-Profile.jpg |50px]] Johanna Forster : Research Area Specialist Intermediate

== Alumni ==

=== Former Research Faculty ===

* Hyun Min Kang (''graduated in 2011''), now Assistant Professor at the [http://www.sph.umich.edu/biostat/ University of Michigan School of Public Health, Department of Biostatistics].

=== Former Research Fellows ===

* Weimin Chen (graduated 2007), now Associate Professor at the [http://people.virginia.edu/~wc9c/ Department of Public Health Sciences & Center for Public Health Genomics, University of Virginia]

* Goo Jun (graduated 2008), now Assistant Professor at the [https://scholar.google.com/citations?user=1wzhcEQAAAAJ&hl=en University of Texas Health Sciences Center]

* Bingshan Li (graudated 2011), now Assistant Professor at the [https://medschool.vanderbilt.edu/cqs/people/Bingshan/Li/cqs-faculty-members Center for Quantitative Sciences, Vanderbilt University]

* [[Dajiang Liu]] (graduated 2013), now Assistant Professor at the [http://www-personal.umich.edu/~dajiang/ Penn State University College of Medicine]

* Serena Sanna (graduated 2007), now an investigator at the [http://www.serenasanna.com/ Istituto di Neurogenetica e Neurofarmacologia in Sardinia, Italy]

* Paul Scheet (graduated 2008), now Associate Professor at [http://faculty.mdanderson.org/Paul_Scheet/Default.asp?SNID=221605974 Department of Epidemiology, University of Texas MD Anderson Cancer Center]

* Carlo Sidore (graduated 2012), now an investigator at the [http://www.cnr.it/istituti/DatiGenerali.html?cds=060 Istituto di Neurogenetica e Neurofarmacologia in Sardinia, Italy]

* Fabio Busonero (graduated 2012), now an investigator at the [http://www.cnr.it/istituti/DatiGenerali.html?cds=060 Istituto di Neurogenetica e Neurofarmacologia in Sardinia, Italy]

* William Stewart (graduated 2008), now Assistant Professor at [http://www.mathmed.org/#William_Stewart Battelle Center for Computational Medicine, Departments of Statistics and Pediatrics, National Children's Hospital and Ohio State University]

* Alex Tsoi (graduated 2014), now Research Assistant Professor at [https://www.med.umich.edu/DERM/faculty/alextsoi_pub.shtml University of Michigan Medical School]

* [[Scott Vrieze]] (graduated 2014), now an Assistant Professor of Psychology and Neuroscience at [http://www.colorado.edu/ibg/people/471 University of Colorado, Boulder]

=== Former Doctoral Students ===

* Wei Chen (graduated 2011), now Assistant Professor at the [http://www.chp.edu/CHP/Chen%2C+Wei%2C+PhD Department of Pediatrics, University of Pittsburgh Medical Center]

* Jun Ding (graduated 2010), now Staff Scientist / Facility Head at the [http://www.grc.nia.nih.gov/branches/lg/lg.htm Laboratory of Genetics, National Institute on Aging (NIH)].

* Shuang Feng (graduated 2015), now Research Scientist at Big Data Lab at Hitachi America Ltd.

* Weihua Guan (graduated 2010), now Assistant Professor at the [http://sph.umn.edu/faculty1/expertise/statistical-genetics/name/weihua-guan/ Department of Biostatistics, University of Minnesota School of Public Health].

* Yun Li (graduated 2009), now Assistant Professor at the [http://www.sph.unc.edu/?option=com_profiles&Itemid=6138&profileAction=ProfDetail&pid=708777879 Department of Biostatistics, University of North Carolina].

* Youna Hu (graduated 2012), now a Data Sciences Engineer at A9, a subsidiary of Amazon.com

* Mingyao Li (graduated 2005), now Associate Professor at the [http://www.cceb.upenn.edu/faculty/index.php?id=159 Department of Biostatistics and Epidemiology, University of Pennsylvania]

* Liming Liang (graduated 2009), now Assistant Professor at the [http://www.hsph.harvard.edu/faculty/liming-liang/ Departments of Biostatistics and Epidemiology, Harvard University]

* Tasha Fingerlin (graduated 2003), now Associate Professor at the [http://www.ucdenver.edu/academics/colleges/PublicHealth/departments/Epidemiology/About/Faculty/Pages/FingerlinT.aspx Section of Epidemiology and Community Health, University of Colorado Health Sciences Center]

* Sara Rashkin (graduated 2015), now Post Doc at [http://wittelab.ucsf.edu/pages/people UCSF Witte Lab]

* Andrew Skol (graduated 2006), now Assistant Professor at the [http://med-www02.bsd.uchicago.edu/339/FacultyPro/faculty_profile.aspx?empl_id=10164 Section of Genetic Medicine, University of Chicago]

* [[Xiaowei Zhan]] (graduated 2014), now Assistant Professor at the [http://profiles.utsouthwestern.edu/profile/152189/xiaowei-zhan.html Department of Clinical Science, University of Texas - Southwestern Medical Center].

* Jin Zhen (graduated 2009), now working in the Pharmaceutical Industry.

=== Former Masters Students ===

* Su Chu

* Melinda Curran

* Vesela Gateva

* Xijing Han

* Dan Hovelson

* Elizabeth Jewell

* Ben Lerch

* Yanming Li

* Heather Munro

* Nick Seewald

* Theresa Scott (nee Daigneault)

* Matthew Snyder

* Vivian Wang

* Yuan Wei

* Abigail Woodroffe

* Zaojun Ye

* Matthew Zawitowski

* Anita Yu Zhao

* Tingting Zhou

=== Former Staff ===

* Paul Anderson

* Laura Baker

* [[Jennifer Bragg-Gresham]]

* Jan Wigginton

=== Visitors ===

* Qing Lu

* Andrea Maschio

* Giorgio Pistis

* Eleanora Porcu

* Toshiko Tanakato

== Really Useful Stuff ==

* [[Abecasis Group Awards]]
* [https://calendars.office.microsoft.com/pubcalstorage/m3n2kr0z1470909/Goncalo_Abecasis_Calendar(1).ics Goncalo's Calendar]

File:PicJingjing.jpg

2016-01-27T18:29:00Z

Amkwong: Amkwong uploaded a new version of "File:PicJingjing.jpg": Changed white balance and cropped

Abecasis Lab

2016-01-27T16:13:38Z

Amkwong: /* Staff */

[[Image:Abecasis2015Retreat.JPG|750px|center|Group Photo 2014]]



== Mission Statement ==

We are developing and applying computational and statistical tools to further understanding of complex human diseases, such as cardiovascular disease and diabetes.

== Leadership ==

[[Goncalo Abecasis]] is currently the Felix Moore Collegiate Professor of Biostatistics at the University of Michigan School of Public Health.

== Current Members ==

=== Research Fellows ===

[[File:Kuser.png|50px]] Christian Fuchsberger

[[File:LarsFritsche_crop.jpg|50px]] [[Lars Fritsche]]

[[File:Kuser.png|50px]] Jingjing Yang

=== Graduate Students ===

[[File:Brieger_Katharine_1.jpg|50px]] Katharine Brieger

[[File:Kuser.png|50px]] Sai Chen

[[File:Kuser.png|50px]] Nate Cohen

[[File:SantyPic.jpeg|50px]] [[Sayantan Das|Sayantan Das]]

[[File:Kuser.png|50px]] Michelle Kleckner

[[File:HeadOfAlanKwong.jpg|50px]] [[Alan Kwong]]

[[File:Kuser.png|50px]] Sebanti Sengupta

[[File:Gregory3.jpg|50px]] Greg Zajac

[[File:Kuser.png|50px]] Fan Zhang

[[File:Kuser.png|50px]] Wanlin Zheng

[[File:Kuser.png|50px]] Wei Zhou

[[File:Xutong.jpg|50px]] Xutong Zhou

=== Staff ===

[[File:Irene_headshot.jpg|50px]] Irene Felicetti : Administrative Assistant Sr.

[[File:TomBlackwell_crop.jpg|50px]] [[Tom Blackwell]] : Research Area Specialist Sr.

[[File:Sean_head.jpg|50px]] [[Sean Caron]] : UNIX Systems Administrator

[[File:Headshot-chris-clark-2 (3).jpg|50px]] Chris Clark : Applications Programmer/Analyst Sr.

[[File:Kevin_Web-Profile.jpg ‎|50px]] Kevin Li : Web Applications Developer

[[File:MK_head.jpg|50px]] [[Mary Kate Wing]] : Applications Programmer working on GotCloud Pipelines, C++ library & tools (libStatGen, bamUtils)

[[File:Johanna_Web-Profile.jpg |50px]] Johanna Forster : Research Area Specialist Intermediate

== Alumni ==

=== Former Research Faculty ===

* Hyun Min Kang (''graduated in 2011''), now Assistant Professor at the [http://www.sph.umich.edu/biostat/ University of Michigan School of Public Health, Department of Biostatistics].

=== Former Research Fellows ===

* Weimin Chen (graduated 2007), now Associate Professor at the [http://people.virginia.edu/~wc9c/ Department of Public Health Sciences & Center for Public Health Genomics, University of Virginia]

* Goo Jun (graduated 2008), now Assistant Professor at the [https://scholar.google.com/citations?user=1wzhcEQAAAAJ&hl=en University of Texas Health Sciences Center]

* Bingshan Li (graudated 2011), now Assistant Professor at the [https://medschool.vanderbilt.edu/cqs/people/Bingshan/Li/cqs-faculty-members Center for Quantitative Sciences, Vanderbilt University]

* [[Dajiang Liu]] (graduated 2013), now Assistant Professor at the [http://www-personal.umich.edu/~dajiang/ Penn State University College of Medicine]

* Serena Sanna (graduated 2007), now an investigator at the [http://www.serenasanna.com/ Istituto di Neurogenetica e Neurofarmacologia in Sardinia, Italy]

* Paul Scheet (graduated 2008), now Associate Professor at [http://faculty.mdanderson.org/Paul_Scheet/Default.asp?SNID=221605974 Department of Epidemiology, University of Texas MD Anderson Cancer Center]

* Carlo Sidore (graduated 2012), now an investigator at the [http://www.cnr.it/istituti/DatiGenerali.html?cds=060 Istituto di Neurogenetica e Neurofarmacologia in Sardinia, Italy]

* Fabio Busonero (graduated 2012), now an investigator at the [http://www.cnr.it/istituti/DatiGenerali.html?cds=060 Istituto di Neurogenetica e Neurofarmacologia in Sardinia, Italy]

* William Stewart (graduated 2008), now Assistant Professor at [http://www.mathmed.org/#William_Stewart Battelle Center for Computational Medicine, Departments of Statistics and Pediatrics, National Children's Hospital and Ohio State University]

* Alex Tsoi (graduated 2014), now Research Assistant Professor at [https://www.med.umich.edu/DERM/faculty/alextsoi_pub.shtml University of Michigan Medical School]

* [[Scott Vrieze]] (graduated 2014), now an Assistant Professor of Psychology and Neuroscience at [http://www.colorado.edu/ibg/people/471 University of Colorado, Boulder]

=== Former Doctoral Students ===

* Wei Chen (graduated 2011), now Assistant Professor at the [http://www.chp.edu/CHP/Chen%2C+Wei%2C+PhD Department of Pediatrics, University of Pittsburgh Medical Center]

* Jun Ding (graduated 2010), now Staff Scientist / Facility Head at the [http://www.grc.nia.nih.gov/branches/lg/lg.htm Laboratory of Genetics, National Institute on Aging (NIH)].

* Shuang Feng (graduated 2015), now Research Scientist at Big Data Lab at Hitachi America Ltd.

* Weihua Guan (graduated 2010), now Assistant Professor at the [http://sph.umn.edu/faculty1/expertise/statistical-genetics/name/weihua-guan/ Department of Biostatistics, University of Minnesota School of Public Health].

* Yun Li (graduated 2009), now Assistant Professor at the [http://www.sph.unc.edu/?option=com_profiles&Itemid=6138&profileAction=ProfDetail&pid=708777879 Department of Biostatistics, University of North Carolina].

* Youna Hu (graduated 2012), now a Data Sciences Engineer at A9, a subsidiary of Amazon.com

* Mingyao Li (graduated 2005), now Associate Professor at the [http://www.cceb.upenn.edu/faculty/index.php?id=159 Department of Biostatistics and Epidemiology, University of Pennsylvania]

* Liming Liang (graduated 2009), now Assistant Professor at the [http://www.hsph.harvard.edu/faculty/liming-liang/ Departments of Biostatistics and Epidemiology, Harvard University]

* Tasha Fingerlin (graduated 2003), now Associate Professor at the [http://www.ucdenver.edu/academics/colleges/PublicHealth/departments/Epidemiology/About/Faculty/Pages/FingerlinT.aspx Section of Epidemiology and Community Health, University of Colorado Health Sciences Center]

* Sara Rashkin (graduated 2015), now Post Doc at [http://wittelab.ucsf.edu/pages/people UCSF Witte Lab]

* Andrew Skol (graduated 2006), now Assistant Professor at the [http://med-www02.bsd.uchicago.edu/339/FacultyPro/faculty_profile.aspx?empl_id=10164 Section of Genetic Medicine, University of Chicago]

* [[Xiaowei Zhan]] (graduated 2014), now Assistant Professor at the [http://profiles.utsouthwestern.edu/profile/152189/xiaowei-zhan.html Department of Clinical Science, University of Texas - Southwestern Medical Center].

* Jin Zhen (graduated 2009), now working in the Pharmaceutical Industry.

=== Former Masters Students ===

* Su Chu

* Melinda Curran

* Vesela Gateva

* Xijing Han

* Dan Hovelson

* Elizabeth Jewell

* Ben Lerch

* Yanming Li

* Heather Munro

* Nick Seewald

* Theresa Scott (nee Daigneault)

* Matthew Snyder

* Vivian Wang

* Yuan Wei

* Abigail Woodroffe

* Zaojun Ye

* Matthew Zawitowski

* Anita Yu Zhao

* Tingting Zhou

=== Former Staff ===

* Paul Anderson

* Laura Baker

* [[Jennifer Bragg-Gresham]]

* Jan Wigginton

=== Visitors ===

* Qing Lu

* Andrea Maschio

* Giorgio Pistis

* Eleanora Porcu

* Toshiko Tanakato

== Really Useful Stuff ==

* [[Abecasis Group Awards]]
* [https://calendars.office.microsoft.com/pubcalstorage/m3n2kr0z1470909/Goncalo_Abecasis_Calendar(1).ics Goncalo's Calendar]

Alan Kwong

2016-01-23T03:45:40Z

Amkwong:

[[Image:HeadOfAlanKwong.jpg|right]]

Alan is a Ph.D. student working with Dr. [[Goncalo Abecasis | Gonçalo Abecasis]] in researching new methods for next-generation sequencing. He earned a B.S. in Bioengineering from University of California, Berkeley, and a M.S. in Biostatistics from the University of Michigan.

Alan has participated in the [[SardiNIA]] project and the [[GotCloud]] project, and is currently working on methods for variant calling for large datasets and the Age-Related Macular Degeneration Whole-Genome Sequencing project and strategies for association studies with multiple phenotypes.

Abecasis Lab

2015-10-19T15:35:31Z

Amkwong:

[[Image:Abecasis2015Retreat.JPG|750px|center|Group Photo 2014]]



== Mission Statement ==

We are developing and applying computational and statistical tools to further understanding of complex human diseases, such as cardiovascular disease and diabetes.

== Leadership ==

[[Goncalo Abecasis]] is currently the Felix Moore Collegiate Professor of Biostatistics at the University of Michigan School of Public Health.

== Current Members ==

=== Research Fellows ===

[[File:Kuser.png|50px]] Christian Fuchsberger

[[File:Kuser.png|50px]] Alex Tsoi

[[File:LarsFritsche_crop.jpg|50px]] [[Lars Fritsche]]

=== International Visitors ===

[[File:Kuser.png|50px]] Andrea Maschio

[[File:Kuser.png|50px]] Giorgio Pistis

[[File:Kuser.png|50px]] Eleanora Porcu

=== Graduate Students ===

[[File:Kuser.png|50px]] Sai Chen

[[File:SantyPic.jpeg|50px]] [[Sayantan Das|Sayantan Das]]

[[File:ShuangFeng1.JPG|50px]] [[Shuang_Feng|Shuang Feng]]

[[File:HeadOfAlanKwong.jpg|50px]] [[Alan Kwong]]

[[File:BenLerch_crop.jpg|50px]] [[Ben Lerch]]

[[File:SaraRashkin_crop.jpg|50px]] [[Sara Rashkin]]

[[File:Kuser.png|50px]] Sebanti Sengupta

[[File:Kuser.png|50px]] Greg Zajac

[[File:Kuser.png|50px]] Tingting Zhou

=== Staff ===

[[File:Laura Head.jpg|50px]] Laura Baker : Administrative Assistant 2008-Present

[[File:TomBlackwell_crop.jpg|50px]] [[Tom Blackwell]]

[[File:Sean_head.jpg|50px]] [[Sean Caron]] : UNIX systems administrator

[[File:Kuser.png|50px]] Kevin Li

[[File:MK_head.jpg|50px]] [[Mary Kate Wing]] : Applications Programmer working on GotCloud Pipelines, C++ library & tools (libStatGen, bamUtils)

[[File:Kuser.png|50px]] Johanna Forster

== Alumni ==

=== Former Research Faculty ===

* Hyun Min Kang (''graduated in 2011''), now Assistant Professor at the [http://www.sph.umich.edu/biostat/ University of Michigan School of Public Health, Department of Biostatistics].

=== Former Research Fellows ===

* Weimin Chen (graduated 2007), now Associate Professor at the [http://people.virginia.edu/~wc9c/ Department of Public Health Sciences & Center for Public Health Genomics, University of Virginia]

* Goo Jun (graduated 2008), now Assistant Professor at the [https://scholar.google.com/citations?user=1wzhcEQAAAAJ&hl=en University of Texas Health Sciences Center]

* Bingshan Li (graudated 2011), now Assistant Professor at the [https://medschool.vanderbilt.edu/cqs/people/Bingshan/Li/cqs-faculty-members Center for Quantitative Sciences, Vanderbilt University]

* [[Dajiang Liu]] (graduated 2013), now Assistant Professor at the [http://www-personal.umich.edu/~dajiang/ Penn State University College of Medicine]

* Serena Sanna (graduated 2007), now an investigator at the [http://www.serenasanna.com/ Istituto di Neurogenetica e Neurofarmacologia in Sardinia, Italy]

* Paul Scheet (graduated 2008), now Associate Professor at [http://faculty.mdanderson.org/Paul_Scheet/Default.asp?SNID=221605974 Department of Epidemiology, University of Texas MD Anderson Cancer Center]

* Carlo Sidore (graduated 2012), now an investigator at the [http://www.cnr.it/istituti/DatiGenerali.html?cds=060 Istituto di Neurogenetica e Neurofarmacologia in Sardinia, Italy]

* Fabio Busonero (graduated 2012), now an investigator at the [http://www.cnr.it/istituti/DatiGenerali.html?cds=060 Istituto di Neurogenetica e Neurofarmacologia in Sardinia, Italy]

* William Stewart (graduated 2008), now Assistant Professor at [http://www.mathmed.org/#William_Stewart Battelle Center for Computational Medicine, Departments of Statistics and Pediatrics, National Children's Hospital and Ohio State University]

* [[Scott Vrieze]] (graduated 2014), now an Assistant Professor of Psychology and Neuroscience at [http://www.colorado.edu/ibg/people/471 University of Colorado, Boulder]

=== Former Doctoral Students ===

* Wei Chen (graduated 2011), now Assistant Professor at the [http://www.chp.edu/CHP/Chen%2C+Wei%2C+PhD Department of Pediatrics, University of Pittsburgh Medical Center]

* Jun Ding (graduated 2010), now Staff Scientist / Facility Head at the [http://www.grc.nia.nih.gov/branches/lg/lg.htm Laboratory of Genetics, National Institute on Aging (NIH)].

* Weihua Guan (graduated 2010), now Assistant Professor at the [http://sph.umn.edu/faculty1/expertise/statistical-genetics/name/weihua-guan/ Department of Biostatistics, University of Minnesota School of Public Health].

* Yun Li (graduated 2009), now Assistant Professor at the [http://www.sph.unc.edu/?option=com_profiles&Itemid=6138&profileAction=ProfDetail&pid=708777879 Department of Biostatistics, University of North Carolina].

* Youna Hu (graduated 2012), now a Data Sciences Engineer at A9, a subsidiary of Amazon.com

* Mingyao Li (graduated 2005), now Associate Professor at the [http://www.cceb.upenn.edu/faculty/index.php?id=159 Department of Biostatistics and Epidemiology, University of Pennsylvania]

* Liming Liang (graduated 2009), now Assistant Professor at the [http://www.hsph.harvard.edu/faculty/liming-liang/ Departments of Biostatistics and Epidemiology, Harvard University]

* Tasha Fingerlin (graduated 2003), now Associate Professor at the [http://www.ucdenver.edu/academics/colleges/PublicHealth/departments/Epidemiology/About/Faculty/Pages/FingerlinT.aspx Section of Epidemiology and Community Health, University of Colorado Health Sciences Center]

* Andrew Skol (graduated 2006), now Assistant Professor at the [http://med-www02.bsd.uchicago.edu/339/FacultyPro/faculty_profile.aspx?empl_id=10164 Section of Genetic Medicine, University of Chicago]

* [[Xiaowei Zhan]] (graduated 2014), now Assistant Professor at the [http://profiles.utsouthwestern.edu/profile/152189/xiaowei-zhan.html Department of Clinical Science, University of Texas - Southwestern Medical Center].

* Jin Zhen (graduated 2009), now working in the Pharmaceutical Industry.

=== Former Masters Students ===

Su Chu

Melinda Curran

Vesela Gateva

Xijing Han

Dan Hovelson

Elizabeth Jewell

Yanming Li

Heather Munro

Nick Seewald

Theresa Scott (nee Daigneault)

Matthew Snyder

Vivian Wang

Yuan Wei

Abigail Woodroffe

Zaojun Ye

Matthew Zawitowski

Anita Yu Zhao

=== Former Staff ===

* Paul Anderson

* [[Jennifer Bragg-Gresham]]

* Jan Wigginton

=== Visitors ===

Toshiko Tanakato

== Really Useful Stuff ==

* [[Abecasis Group Awards]]
* [https://calendars.office.microsoft.com/pubcalstorage/m3n2kr0z1470909/Goncalo_Abecasis_Calendar(1).ics Goncalo's Calendar]

Main Page

2015-07-28T00:44:02Z

Amkwong: Updated group photo with 2015 version

<div id="mf-mainpage">


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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>
|}

[[Image:Abecasis2015Retreat.JPG|700px|center|Group Photo 2015]]





== Welcome! ==

Welcome to our brand new 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 ==

[[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>

File:Abecasis2015Retreat.JPG

2015-07-28T00:41:52Z

Amkwong:

Alan Kwong

2014-06-03T17:43:36Z

Amkwong:

[[Image:HeadOfAlanKwong.jpg|right]]

Alan is a Ph.D. student working with Dr. [[Goncalo Abecasis]] in researching new methods for next-generation sequencing. He earned a B.S. in Bioengineering from University of California, Berkeley, and a M.S. in Biostatistics from the University of Michigan.

Alan has participated in the [[SardiNIA]] project and the [[GotCloud]] project, and is currently working on methods for variant calling for large datasets and the Age-Related Macular Degeneration Whole-Genome Sequencing project.

Alan Kwong

2013-06-14T16:16:30Z

Amkwong:

Alan Kwong

2013-06-14T16:15:47Z

Amkwong: Created page with 'right Alan is a Ph.D. student working with Dr. Goncalo Abecasis in researching new methods for next-generation sequencing. He earned a B.S. in …'

2013-01-10T05:44:49Z

Amkwong:

==Installation==

First, make sure GotCloud is installed on your system. Installation instructions [[GotCloud#Setup|here]].

==Running the Automatic Test==

This verifies that GotCloud was installed correctly.

To run the test case automatically, change your current directory to GotCloud's root directory, and type in the following command:

bin/gen_biopipeline.pl --test OUTPUT_DIR

where OUTPUT_DIR is the directory where you want to store the results.

If you see "Test Passed", then you are ready to run a sample.

==Aligning a Sample==

As an example, we can align the sample fastq files used in the automatic test. They belong to two different samples, which we will call "Sample1" and "Sample2". They are found in {ROOT_DIR}/test/align/fastq. (We will call the directory in which GotCloud is installed "{ROOT_DIR}".)

To make this easier, change to the {ROOT_DIR}/test/align directory. It contains an index file and a configuration file that can be used directly.

===Index file===

There are four fastq files in {ROOT_DIR}/test/align/fastq/Sample_1 and four fastq files in {ROOT_DIR}/test/align/fastq/Sample_2, both in paired-end format. Normally, we would need to build an index file for these files. Conveniently, an index file (indexFile.txt) already exists for the automatic test samples. It can be found in {ROOT_DIR}/test/align/, and contains the following information in tab-delimited format:

MERGE_NAME FASTQ1 FASTQ2 RGID SAMPLE LIBRARY CENTER PLATFORM
Sample1 fastq/Sample_1/File1_R1.fastq.gz fastq/Sample_1/File1_R2.fastq.gz RGID1 SampleID1 Lib1 UM ILLUMINA
Sample1 fastq/Sample_1/File2_R1.fastq.gz fastq/Sample_1/File2_R2.fastq.gz RGID1a SampleID1 Lib1 UM ILLUMINA
Sample2 fastq/Sample_2/File1_R1.fastq.gz fastq/Sample_2/File1_R2.fastq.gz RGID2 SampleID2 Lib2 UM ILLUMINA
Sample2 fastq/Sample_2/File2_R1.fastq.gz fastq/Sample_2/File2_R2.fastq.gz RGID2 SampleID2 Lib2 UM ILLUMINA

If you are in the {ROOT_DIR}/test/align directory, you can use this file as-is. If you prefer, you can create a new index file and change the MERGE_NAME, RGID, SAMPLE, LIBRARY, CENTER, or PLATFORM values. It is recommended that you do not modify existing files in {ROOT_DIR}/test/align.

If you want to run this example from a different directory, make sure the FASTQ1 and FASTQ2 paths are correct. That is, each of the FASTQ1 and FASTQ2 entry in the index file should look like the following:

{ROOT_DIR}/test/align/fastq/Sample_1/File1_R1.fastq.gz

Alternately, if you want to run this example from a different directory, but do not want to edit the index file, you can copy all the fastq files to a new directory with the relative path listed in the index file:

ln -s {ROOT_DIR}/test/align/fastq fastq

This will create a symbolic link to the test fastq directory from your current directory.

(More information about: [[Mapping_Pipeline#Sequence_Index_File|the index file]].)

===Configuration file===

Similar to the index file, a configuration file (test.conf) already exists for the automatic test samples. It contains the following information:

INDEX_FILE = indexFile.txt
############
# References
REF_DIR = $(PIPELINE_DIR)/test/align/chr20Ref
AS = NCBI37
FA_REF = $(REF_DIR)/human_g1k_v37_chr20.fa
DBSNP_VCF = $(REF_DIR)/dbsnp.b130.ncbi37.chr20.vcf.gz
PLINK = $(REF_DIR)/hapmap_3.3.b37.chr20

If you are in the {ROOT_DIR}/test/align directory, you can use this file as-is. If you are using a different index file, make sure your index file is named correctly in the first line. If you are not running this from {ROOT_DIR}/test/align, make sure your configuration and index files are in the same directory.

(More information about: [[Mapping_Pipeline#Reference_Files|reference files]], [[Mapping_Pipeline#Optional_Configurable_Settings|optional configurable settings]], or [[Mapping_Pipeline#Command-Line_Options|command-line options]].)

===Running the alignment pipeline===

You are now ready to run the alignment pipeline. This requires two steps: first, generating the Makefiles; and second, running those Makefiles.

====Generating the Makefiles====

Enter the following command:

{ROOT_DIR}/bin/gen_biopipeline.pl --conf test.conf --out_dir {OUT_DIR}

where {OUT_DIR} is the directory in which you wish to store the resulting BAM files (for example, ~/out).

If everything went well, you will see the following messages:

Finished creating makefile {OUT_DIR}/Makefiles/biopipe_Sample2.Makefile
Finished creating makefile {OUT_DIR}/Makefiles/biopipe_Sample1.Makefile
--------------------------------------------------------------------
Run the following commands:

make -f {OUT_DIR}/Makefiles/biopipe_Sample2.Makefile > {OUT_DIR}/Makefiles/biopipe_Sample2.Makefile.log
make -f {OUT_DIR}/Makefiles/biopipe_Sample1.Makefile > {OUT_DIR}/Makefiles/biopipe_Sample1.Makefile.log

where {OUT_DIR} will be replaced with the directory you entered above.

====Running the Makefiles====

To run a Makefile, simply enter one-by-one the commands generated in the previous step. If you wish to run the alignment in the background, add "&" after the make command, as follows:

make -f {OUT_DIR}/Makefiles/biopipe_Sample2.Makefile > {OUT_DIR}/Makefiles/biopipe_Sample2.Makefile.log &

The log files for the runs will be found in the Makefiles directory, while the BAM files will be found in the {OUT_DIR}/alignment.recal directory. If you see two BAM files, one for each sample, then you have successfully aligned the fastq files.

==Analyzing a Sample==

Using UMAKE, you can analyze BAM files by calling SNPs, and generate a VCF file containing the results. Once again, we can analyze BAM files used in the automatic test. For this example, we have 60 BAM files, found in {ROOT_DIR}/test/umake/bams. In addition to the BAM files, you will need three files to run UMAKE: an index file, a configuration file, and a bed file.

===Index file===

First, you need a list of all the BAM files to be analyzed. Conveniently, the a test index file (umake_test.index) already exists in {ROOT_DIR}/test/umake/. It contains the following information:

NA12272 ALL bams/NA12272.mapped.ILLUMINA.bwa.CEU.low_coverage.20101123.chrom20.20000001.20300000.bam
NA12004 ALL bams/NA12004.mapped.ILLUMINA.bwa.CEU.low_coverage.20101123.chrom20.20000001.20300000.bam
...
NA12874 ALL bams/NA12874.mapped.LS454.ssaha2.CEU.low_coverage.20101123.chrom20.20000001.20300000.bam

You can use this file directly if you change your current directory to {ROOT_DIR}/test/umake/.

Alternately, if you want to copy and use this index file to a different directory, you can create a symbolic link to the bams folder as follows:

ln -s {ROOT_DIR}/test/umake/bams bams

(More information about: [[Variant_Calling_Pipeline_(UMAKE)#Index_File|the index file]].)

===BED file===

This file contains a single line:

chr20 20000050 20300000

You can copy this to the current directory and use it as-is.

(More information about: [[Variant_Calling_Pipeline_(UMAKE)#Targeted.2FExome_Sequencing_Settings|targeted/exome sequencing settings]].)

===Configuration file===

A configuration file (umake_test.conf) already exists in {ROOT_DIR}/test/umake/. It contains the following information:

CHRS = 20
TEST_ROOT = $(UMAKE_ROOT)/test/umake
BAM_INDEX = $(TEST_ROOT)/umake_test.index
OUT_PREFIX = umake_test
REF_ROOT = $(TEST_ROOT)/ref
#
REF = $(REF_ROOT)/karma.ref/human.g1k.v37.chr20.fa
INDEL_PREFIX = $(REF_ROOT)/indels/1kg.pilot_release.merged.indels.sites.hg19
DBSNP_PREFIX = $(REF_ROOT)/dbSNP/dbsnp_135_b37.rod
HM3_PREFIX = $(REF_ROOT)/HapMap3/hapmap3_r3_b37_fwd.consensus.qc.poly
#
RUN_INDEX = TRUE # create BAM index file
RUN_PILEUP = TRUE # create GLF file from BAM
RUN_GLFMULTIPLES = TRUE # create unfiltered SNP calls
RUN_VCFPILEUP = TRUE # create PVCF files using vcfPileup and run infoCollector
RUN_FILTER = TRUE # filter SNPs using vcfCooker
RUN_SPLIT = TRUE # split SNPs into chunks for genotype refinement
RUN_BEAGLE = FALSE # BEAGLE - MUST SET AFTER FINISHING PREVIOUS STEPS
RUN_SUBSET = FALSE # SUBSET FOR THUNDER - MAY BE SET WITH BEAGLE STEP TOGETHER
RUN_THUNDER = FALSE # THUNDER - MUST SET AFTER FINISHING PREVIOUS STEPS
###############################################################################
WRITE_TARGET_LOCI = TRUE # FOR TARGETED SEQUENCING ONLY -- Write loci file when performing pileup
UNIFORM_TARGET_BED = $(TEST_ROOT)/umake_test.bed # Targeted sequencing : When all individuals has the same target. Otherwise, comment it out
OFFSET_OFF_TARGET = 50 # Extend target by given # of bases
MULTIPLE_TARGET_MAP = # Target per individual : Each line contains [SM_ID] [TARGET_BED]
TARGET_DIR = target # Directory to store target information
SAMTOOLS_VIEW_TARGET_ONLY = TRUE # When performing samtools view, exclude off-target regions (may make command line too long)

If you are running this from a different directory, you will want to change some of the lines as follows:

BAM_INDEX = {CURRENT_DIR}/umake_test.index
UNIFORM_TARGET_BED = {CURRENT_DIR}/umake_test.bed

where {CURRENT_DIR} is the absolute path to the directory that contains the index and bed files.

An additional option can be added in the configuration file:

OUT_DIR = {OUT_DIR}

where {OUT_DIR} is the name of directory in which you want the output to be stored. If you do not specify this in the configuration file, you will need to add an extra parameter when you run UMAKE in the next step.

(More information about: [[Variant_Calling_Pipeline_(UMAKE)#Configuration_File|the configuration file]], [[Variant_Calling_Pipeline_(UMAKE)#Reference_Files|reference files]].)

===Running UMAKE===

If you added an OUT_DIR line to the configuration file, you can run UMAKE with the following command:

{ROOT_DIR}/bin/umake.pl --conf umake_test.conf --snpcall --numjobs 2

If you have not added an OUT_DIR line to the configuration file, you can specify the output directory directly with the following command:

{ROOT_DIR}/bin/umake.pl --conf umake_test.conf --outdir {OUT_DIR} --snpcall --numjobs 2

where {OUT_DIR} is the directory in which you want the output to be stored.

Either command will perform SNP calling on the test samples. If you find the resulting VCF files located in {OUT_DIR}/vcfs/chr20, then you have successfully called the SNPs from the test BAM files.

==Further Information==

[[Mapping_Pipeline|Mapping (Alignment) Pipeline]]

[[Variant_Calling_Pipeline_(UMAKE)|Variant Calling Pipeline (UMAKE)]]