Difference between revisions of "Mach DAC"

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This is the MaCH Divide and Conquer page, documenting how to break the genome into smaller pieces before imputation/phasing and how to ligate after imputation/phasing.
 
This is the MaCH Divide and Conquer page, documenting how to break the genome into smaller pieces before imputation/phasing and how to ligate after imputation/phasing.
  
== Phase without External Reference ==
+
== Phasing without External Reference ==
 
=== Your Data ===
 
=== Your Data ===
 
To get started, you will need to store your data in [[Merlin]] format pedigree and data files, one per chromosome. For details of the Merlin file format, see the Merlin tutorial [http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html]. <br>
 
To get started, you will need to store your data in [[Merlin]] format pedigree and data files, one per chromosome. For details of the Merlin file format, see the Merlin tutorial [http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html]. <br>
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You can split your data using [http://www.sph.umich.edu/csg/yli/splitPed/ splitPed].
 
You can split your data using [http://www.sph.umich.edu/csg/yli/splitPed/ splitPed].
  
== Phase/Imputation with External Reference ==
+
== Phasing/Imputation with External Reference ==
 +
When you phase/impute with external reference panel, you will only need to break the reference files into parts containing subsets of markers because SNPs in your own data (pedigree files) but not in reference files will be automatically ignored by MaCH and minimac. <br>
 +
 
 +
You can split the reference files using [http://www.sph.umich.edu/csg/yli/splitPed/ splitHap].
 +
 
 +
== Post Phasing/Imputation Ligation ==
 +
 
 +
 
  
 
== Questions and Comments?  ==
 
== Questions and Comments?  ==
  
 
Email [mailto:yunli@med.unc.edu Yun Li].
 
Email [mailto:yunli@med.unc.edu Yun Li].

Revision as of 15:33, 29 November 2010

This is the MaCH Divide and Conquer page, documenting how to break the genome into smaller pieces before imputation/phasing and how to ligate after imputation/phasing.

Phasing without External Reference

Your Data

To get started, you will need to store your data in Merlin format pedigree and data files, one per chromosome. For details of the Merlin file format, see the Merlin tutorial [1].

Within each file, markers should be stored by chromosome position. Alleles should be stored in the forward strand and can be encoded as 'A', 'C', 'G' or 'T' (there is no need to use numeric identifiers for each allele).

Split Your Data

You can split your data using splitPed.

Phasing/Imputation with External Reference

When you phase/impute with external reference panel, you will only need to break the reference files into parts containing subsets of markers because SNPs in your own data (pedigree files) but not in reference files will be automatically ignored by MaCH and minimac.

You can split the reference files using splitHap.

Post Phasing/Imputation Ligation

Questions and Comments?

Email Yun Li.