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=== MaCH ===
=== MaCH ===
'''MaCH''' is a Markov Chain based haplotyper. It can resolve long haplotypes in samples of unrelated individuals. The source code is available for download here. Check out there [http://www.sph.umich.edu/csg/abecasis/MaCH/ home-page] for further details.
'''MaCH''' is a Markov Chain based haplotyper. It can resolve long haplotypes in samples of unrelated individuals. The source code is available for download [http://www.sph.umich.edu/csg/abecasis/MaCH/download/ here]. Check out their [http://www.sph.umich.edu/csg/abecasis/MaCH/ home-page] for further details.
A typical command line to phase using MaCH looks like this
A typical command line to phase using MaCH looks like this (<code>Gwas.chr20.Unphased.dat</code> and <code>Gwas.chr20.Unphased.ped </code> is the quality controlled GWAS data set in [http://www.sph.umich.edu/csg/abecasis/Merlin/ Merlin] format)
mach1 -d Gwas.chr20.Unphased.dat \
mach1 -d Gwas.chr20.Unphased.dat \
=== SHAPEIT===
=== SHAPEIT===
'''SHAPEIT''' is a fast and accurate method for estimation of haplotypes (phasing) from genotype or sequencing data. The source code is available for download here. Check out there [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html home-page] for further details.
'''SHAPEIT''' is a fast and accurate method for estimation of haplotypes (phasing) from genotype or sequencing data. The source code is available for download [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#download here]. Check out their [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html home-page] for further details. It can be used to phase a small number of samples (a reference panel required) as well as a large number of samples (NO reference panel required). The reference panels and genetic map files required by SHAPEIT are available for download [https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#reference here].
* The following example shows a typical SHAPEIT command line to phase a LARGE number (>200) of GWAS samples (<code>Gwas.chr20.Unphased.vcf</code> is the quality controlled GWAS data set in VCF format).
* The following example shows a typical SHAPEIT command line to phase a LARGE number (>200) of GWAS samples (<code>Gwas.chr20.Unphased.vcf</code> is the quality controlled GWAS data set in VCF format).
