I guess first I should make sure I understand how GEDmatch stores raw data -- I'd guess that during "tokenization", GEDmatch turns my raw data file into a format that it likes, i.e., perhaps replacing A, T, G, C with numbers or replacing names of loci with numbers, etc. And because raw data comes from different companies in different forms, this process "standardizes" the information GEDmatch is using. But I assume it is equivalent to having the information in my file -- i.e., a list of loci names, corresponding chromosome and position, and a pair of nucleotides, i.e., A, T, G, or C. Is this essentially correct?
I saw recently on another forum a description of what GEDmatch does to create a psuedo-kit phased between a parent and child:
"They are then simply taking the SNP differences between the child's kit and the parent's kit, removing those alleles of the tested parent that can be confirmed to be necessarily present in the other parent, removing any no-calls, and creating the new "pseudo kit" from those values...which will always have decidedly fewer SNPs than actual raw test results. "
Here's what I draw from this post:
As I understand it, a phased parent/child kit is a substitute for the child's kit. The idea is that the substitute will reveal matches to the child known to be on that parent's side. It sounds like data is stored as pairs of alleles, and when a single allele in the child does not match either allele of the corresponding pair in the given parent, it is attributed to the other parent and stripped out, and no-calls are stripped out as well.
Is this roughly what the phased kit will contain? Then here's the problem I can't wrap my brain around: I would guess less than half of the alleles would be removed since one allele in each pair for the child DID come from the given parent and sometimes both parents would have matching alleles by chance (Also I presume the no-call percentage is just a few percent).
Using GEDmatch Genesis, I phased my kit with my mother's (hers was uploaded to GEDmatch) and saw the number of tokens decrease from 450000 to 190000 in the phased pseudo-kit. Perhaps this has something to do with Genesis being in beta and the kits being on the different sites, but I've heard reports of SNP counts dropping almost 10-fold between a kit and a pseudo kit. And in my own case, the number of tokens used used for chromosome 1 dropped from 37969 to 0 after phasing!
What is wrong with my understanding and accounts for these huge drops in amounts of data?