Haplotype construction based on SNPs with haploview

Question

[Ripeapple]

Hi, all,

I am having problem with the input file format for Haploview. My samples are unrelated individuals so I don't have any linkage or pedigree information. I do have the hapmap file that contains the position, chromosome information of each SNP and the alleles in each individual.

As I 'm new to this software, can anyone tell me what kind of format I should convert my SNP file to and what is the best way to infer haplotypes?

Any help would be tremendously appreciated!!!

Answer 1

[Floris Brenk]

I think they have a good description what input files you can use or what you should change in the manual.

When still have trouble after reading/doing this please post a example of what format you have.

[Ripeapple]

Hi, thanks a lot for the reply!

I guess my question is what format should I use. The information I have is as following:

Marker     Chromosome     Position     Individual1     Individual2     Individual3     Individual4     Individual5
3241       Chr01          3241         CT              CC              CT              TT              CT
3280       Chr01          3280         AT              TT              AT              TA              AA

Do you have any suggestions? Thanks

Answer 2

[viavialin]

For your purpose, I think that the Linkage Format would be the best. I have done similar analysis using both Linkage Format and HapMap Format.

Data file : Should be in the format - Ped ID, Indiv ID, Father ID, Mother ID, Sex, Outcome, x2 Alleles. (as described in the link provided above

Locus information : rs#, chromosome position

For example your data file should look like this- (without headers)

PedID IndividualID FatherID   MotherID Sex  Outcome  Allele1  Allele2  Allele1  Allele 2
XX    1            0          0        1    1        C        T        A        T
XX    2            0          0        1    1        C        C        T        T

etc

The locus info should correspond to order of the SNPs in the data file

Marker  chr_position
3241    100,000,000
3280    100,000,001

I have only used the HapMap format when I have the dumped file downloaded from International HapMap project database.

Hope this helps!

[Ripeapple]

Thank you so much, The format works,