Can someone explain haplotype phase, or phasing software? Or is phasing a slang term?
This is what Montgomery Slatkin says athttp://www.nature.com/nrg/journal/v9/n6/box/nrg2361_BX2.html
"The basic idea is that individuals that are homozygous at all loci or all but one locus provide some information about haplotype frequencies that can then be used to infer the haplotype phase of the other individuals."
This sounds like something we are already doing here albeit on a primitive level.
"There are several ways to determine haplotypes from genotypes; this is commonly referred to as resolving haplotype phase." He says that the program PHASE has performed the best in simulation studies.
When I look at my X results for the area including the centromere, I have many heterozygous readings, but if I pick the two most common haplotypes from all the male results, my parents fit very nicely just by guessing the most likely ones. Now would that also be called a way of resolving possible haplotype phase?
Sorry for the delayed response... I tried to answer this question a couple of days ago, but website glitches prevented me from being able to login...
Phasing isn't a slang term, it just means the process of trying to determine which DNA came from which chromosome of a homologous pair (i.e., determining which came from the mother, and which came from the father, as you've been doing).
Ann Turner has a good writeup of this concept here:http://www.jogg.info/42/files/turner.pdf
Your guessing-based-on-common-results-from-males is one way of phasing, though I have no idea how the accuracy of that method compares with using programs like PHASE.