Question: Input File Formats in Haploview
1
gravatar for jgocejo
2.3 years ago by
jgocejo10
Spain
jgocejo10 wrote:

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

minia assembly • 1.3k views
ADD COMMENTlink written 2.3 years ago by jgocejo10
1

the tags for this question seem off :)

ADD REPLYlink written 2.3 years ago by Rayan Chikhi1.2k
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