Calculates multi–locus haplotype frequencies (two or more loci) or allele frequencies under two alternative models (either Hardy-Weinberg equilibrium or inbreeding–like).
Read more about these tools (and see examples of input files) in the usage overview.
The estimation uses the Hardy-Weinberg expected proportions by default, but can be set to include the inbreeding coefficient (F).
Output can include alternative genotypes and their respective probabilities for phenotypes that lead to ambigous genotypes.
Input must be a valid UNIFORMAT file with .unif extension.
Greetings. I am failing to use the FREE tool on my data set. I successfully converted my excel file to uniformat but seem not be able to do allele and haplotype frequency calculations. May you kindly help, I herewith paste a small portion of my data set I formatted according to the 2012 HLA-NET tutorial. Some individuals in the data set have missing allele data (maybe a reason why I can not analyse the data.
I plan to calculate allele and haplotype frequencies and use the regional and chart tools of the HLA-NET
I thank you in advance
Sincerely
[…]
sample ID A1, A2, B1, B2, C1, C2, DRB1, DRB1, DQB1, DQB1, DPB1, DPB1, , , , , , , , , , ,
NHLS00001 ,; ,| 7,; ,| ,; ,| ,; ,| ,; ,| ,; ,| , , , , , , , , , ,
NHLS00002 ,; 68,| ,; ,| ,; ,| ,; ,| ,; ,| ,; ,| , , , , , , , , , ,
NHLS00003 ,; ,| ,; ,| ,; ,| 13,; ,| ,; ,| ,; ,| , , , , , , , , , ,
NHLS00004 2,; 28,| 44,; 15,| ,; ,| ,; ,| ,; ,| ,; ,| , , , , , , , , , ,
NHLS00005 ,; ,| ,; ,| ,; ,| ,; ,| 5,; ,| ,; ,| , , , , , , , , , ,
NHLS00006 1,; 25,| 8,; ,| ,; ,| ,; ,| ,; ,| ,; ,| , , , , , , , , , ,
NHLS00007 ,; ,| ,; ,| ,; ,| 7,; ,| ,; ,| ,; ,| , , , , , , , , , ,
NHLS00008 ,; ,| ,; ,| ,; ,| 411,; ,| ,; ,| ,; ,| , , , , , , , , , ,
I guess we have already solved the issues raised here after mail conversation, it was a format problem.
An easy way to get over this kind of problems it is to start with a very tiny data set (only a few cases) and see if calculations go, if it works on the small it should also work on large and even on very large data sets.