Input File Formats in Haploview

Question

[jgocejo]

First of all, sorry for any inconvenience and thanks in advance for your consideration. I am trying to analyse haplotype frequencies and associations

by using Haploview (it is the first time I use it), and I do not understand / know how to do it: I have 4 SNPs (C/T, C/A, C/G and AC). The Phased haplotypes input file format seems to be the easiest (at least for me):

FAM1    FAM1M01    0    4    2    2
FAM1    FAM1M01    0    4    2    2
FAM1    FAM1F02    3    h    1    2
FAM1    FAM1F02    3    h    1    2

There are two lines (chromosomes) for each individual, 0 represents missing data, and h a heterozygous allele, but how can I assign the 1-4 numbers to the different genotypes?:

1 CC CC CC AA, 2 CC AA CC AA, 3 CC CC GG AA, 4 CC CC CC CC

And the rest of genotypes? (for example TT CC CC AA, TT AA GG CC, etc?)

Thanks a lot!

jg

[Rayan Chikhi]

the tags for this question seem off :)