Genome Analysis Wiki - User contributions [en]

Mach2dat: Association with MACH output

2010-08-30T02:21:27Z

Sannas: /* Association with MACH output */

== Association with MACH output ==

After you have performed the imputation, you can directly use MACH output to assess association for quantitative and qualitative traits in unrelated.

You will need the *.ped and *.dat files in Merlin format[http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html] to specify the disesase status or quantitative trait of interest (indicated with A and T respectively in the dat file).

Then, you can run the association using the following command line:

mach2dat -p myfile.ped -d myfile.dat --infofile myfile.mlinfo --dosefile myfile.mldose

where myfile.mlinfo and myfile.mldose are the MACH output files.

You can also add covariates to the phenotype *ped and *dat files if you want to adjust your test for other variables.

*Please note that mach2dat analyze only unrelated samples. If you input a pedigree with family relationship, those will be ignored.

If you have family data, you can use merlin-offline [http://www.sph.umich.edu/csg/abecasis/merlin/index.html]

Mach2dat: Association with MACH output

2010-08-30T02:20:56Z

Sannas: /* Association with MACH output */

== Association with MACH output ==

After you have performed the imputation, you can directly use MACH output to assess association for quantitative and qualitative traits in unrelated.

You will need the *.ped and *.dat files in Merlin format[http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html] to specify the disesase status or quantitative trait of interest (indicated with A and T respectively in the dat file).

Then, you can run the association using the following command line:

mach2dat -p myfile.ped -d myfile.dat --infofile myfile.mlinfo --dosefile myfile.mldose

where myfile.mlinfo and myfile.mldose are the MACH output files.

You can also add covariates to the phenotype *ped and *dat files if you want to adjust your test for other variables.

*Please note that mach2dat analyze only unrelated samples. If you input family relationship, those will be ignored.

If you have family data, you can use merlin-offline [http://www.sph.umich.edu/csg/abecasis/merlin/index.html]

Mach2dat: Association with MACH output

2010-08-30T02:20:05Z

Sannas: /* Association with MACH output */

== Association with MACH output ==

After you have performed the imputation, you can directly use MACH output to assess association for quantitative and qualitative traits in unrelated.

You will need the *.ped and *.dat files in Merlin format[http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html] to specify the disesase status or quantitative trait of interest (indicated with A and T respectively in the dat file)

mach2dat -p myfile.ped -d myfile.dat --infofile myfile.mlinfo --dosefile myfile.mldose

where myfile.mlinfo and myfile.mldose are the MACH output files.

You can also add covariates to the phenotype *ped and *dat files if you want to adjust your test for other variables.

*Please note that mach2dat analyze only unrelated samples. If you input family relationship, those will be ignored.

If you have family data, you can use merlin-offline [http://www.sph.umich.edu/csg/abecasis/merlin/index.html]

Mach2dat: Association with MACH output

2010-08-30T02:18:49Z

Sannas: Created page with '== Association with MACH output == After you have performed the imputation, you can directly use MACH output to assess association for quantitative and qualitative traits in un…'

== Association with MACH output ==

After you have performed the imputation, you can directly use MACH output to assess association for quantitative and qualitative traits in unrelated.

You will need a *.ped and *.dat files in Merlin format[http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html] that contain the disesase status or quantitative trait of interest (indicated with A and T respectively in the dat file)

mach2dat -p myfile.ped -d myfile.dat --infofile myfile.mlinfo --dosefile myfile.mldose

where myfile.mlinfo and myfile.mldose are the MACH output files.

You can also add covariates to the phenotype *ped and *dat files if you want to adjust your test for other variables.

*Please note that mach2dat analyze only unrelated samples. If you input family relationship, those will be ignored.

If you have family data, you can use merlin-offline [http://www.sph.umich.edu/csg/abecasis/merlin/index.html]

MaCH

2010-08-30T02:16:24Z

Sannas:

'''MaCH''' is a tool for haplotyping, genotype imputation and disease association analysis developed by Goncalo Abecasis and Yun Li. MaCH was first used to imputed missing genotypes in our FUSION genomewide association study ([http://www.sph.umich.edu/csg/abecasis/publications/17463248.html Scott et al, ''Science'', 2007]) and has since been used in the analysis of many other GWAS.

This page includes links to several useful MaCH related resources.

* The main MaCH webpage at http://www.sph.umich.edu/csg/abecasis/MaCH/
* The MaCH download page, with source code, executables and reference haplotype files at http://www.sph.umich.edu/csg/abecasis/MaCH/download/
* The MaCH tutorial at http://www.sph.umich.edu/csg/abecasis/MaCH/tour/
* [[MaCH FAQ|The MaCH FAQ]]
* [[MaCH Options|MaCH Options]]
* [[MaCH: Input Files|Information on MaCH input formats]]
* [[MaCH: 1000 Genomes Imputation Cookbook|1000 Genomes Imputation Cookbook]]
* [[Mach2dat: Association with MACH output]]

Currently, it also includes random notes on input file formats, but these probably need to be cleaned up!

MaCH

2010-08-30T02:05:07Z

Sannas:

'''MaCH''' is a tool for haplotyping, genotype imputation and disease association analysis developed by Goncalo Abecasis and Yun Li. MaCH was first used to imputed missing genotypes in our FUSION genomewide association study ([http://www.sph.umich.edu/csg/abecasis/publications/17463248.html Scott et al, ''Science'', 2007]) and has since been used in the analysis of many other GWAS.

This page includes links to several useful MaCH related resources.

* The main MaCH webpage at http://www.sph.umich.edu/csg/abecasis/MaCH/
* The MaCH download page, with source code, executables and reference haplotype files at http://www.sph.umich.edu/csg/abecasis/MaCH/download/
* The MaCH tutorial at http://www.sph.umich.edu/csg/abecasis/MaCH/tour/
* [[MaCH FAQ|The MaCH FAQ]]
* [[MaCH Options|MaCH Options]]
* [[MaCH: Input Files|Information on MaCH input formats]]
* [[MaCH: 1000 Genomes Imputation Cookbook|1000 Genomes Imputation Cookbook]]
* [[Mach2dat: analyze case-control data with MACH output]]

Currently, it also includes random notes on input file formats, but these probably need to be cleaned up!

Abecasis Lab

2010-08-22T00:54:30Z

Sannas: /* Former Research Fellows */

[[Image:2009.08_Group_Retreat_Photo.jpg|400px|center|Group Photo]]

== Mission Statement ==

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

== Current Members ==

=== Research Faculty ===

Hyun Min Kang

=== Research Fellows ===

Bingshan Li

Christian Fuchsberger

=== International Visitors ===

Fabio Busonero

Carlo Sidore

=== Graduate Students ===

Wei Chen

Melinda Curran

Jun Ding

Dan Hovelson

Youna Hu

Elizabeth Jewell

Yanming Li

Sara Rashkin

Shuang Feng

Matthew Snyder

Xiaowei Zhan

=== Staff ===

Paul Anderson

Laura Baker

Tom Blackwell

Jennifer Bragg-Gresham

Derek Harkness

Mary Kate Trost

== Alumni ==

=== Former Research Fellows ===

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

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 Assistant Professor at [http://faculty.mdanderson.org/Paul_Scheet/Default.asp?SNID=221605974 Department of Epidemiology, University of Texas MD Anderson Cancer Center]

William Stewart (graduated 2008), now Assistant Professor at [http://www.columbia.edu/~ws2267/ Department of Biostatistics, Columbia University]

=== Former Doctoral Students ===

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].

Mingyao Li (graduated 2005), now Assistant 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://pmb.uchsc.edu/faculty/Fingerlin/index.html 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/FacultyProfile/faculty_profile.aspx?empl_id=10164 Section of Genetic Medicine, University of Chicago]

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

=== Former Masters Students ===

Xijing Han

Heather Munro

Theresa Scott (nee Daigneault)

Abigail Woodroffe

Zaojun Ye

Matthew Zawitowski

Anita Yu Zhao

=== Visitors ===

Toshiko Tanakato

== Really Useful Stuff ==

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