Changes

A typical command line to phase using MaCH looks like this

A typical command line to phase using MaCH looks like this

  mach1 -d chr1.dat \

  mach1 -d Gwas.chr20.Unphased.dat \

       -p chr1.ped \

       -p Gwas.chr20.Unphased.ped \

       --rounds 20 \

       --rounds 20 \

       --states 200 \

       --states 200 \

=== SHAPEIT===

=== SHAPEIT===

'''SHAPEIT''' 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.

'''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.

A typical command line to phase using MaCH looks like this

SHAPEIT 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 are available for download on their [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html home-page].

mach1 -d chr1.dat \

* The following example shows a typical SHAPEIT command line to phase a large number of GWAS samples (<code>Gwas.chr20.Unphased.vcf</code> is the quality control GWAS data set in VCF format).

      -p chr1.ped \

 

shapeit -V Gwas.chr20.Unphased.vcf \

      --states 200 \

        -M genetic_map_chr20.txt \

      --phase \

        -O Gwas.Chr20.Phased.Output

      --interim 5 \

      --prefix Gwas.Chr20.Phased.Output

= Chromosome X Imputation =

= Chromosome X Imputation =