Changes

== Estimating Haplotypes for Your Sample ==

== Estimating Haplotypes for Your Sample ==

For the haplotyping step, you can use [[MaCH]] with the --phase command line option. As input [[MaCH]] will need [[Merlin]] format pedigree and data files. All markers should be ordered according to their physical position and alleles should be labeled on the forward strand.  

For the haplotyping step, you can use [[MaCH]] with the --phase command line option or [[https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html ShapeIT]. As input [[MaCH]] will need [[Merlin]] format pedigree and data files. All markers should be ordered according to their physical position and alleles should be labeled on the forward strand.  

=== Preparing Your Data ===

=== Preparing Your Data ===