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Haplotype construction based on SNPs with haploview

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!!!

snp haploview
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updated by Ram Ram • written by Ripeapple • Ripeapple

2 answers

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.

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updated by Ram Ram • written by Floris Brenk Floris Brenk

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

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updated by Ram Ram • written by Ripeapple • Ripeapple

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!

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updated by Ram Ram • written by viavialin • viavialin

Thank you so much, The format works,

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written by Ripeapple • Ripeapple

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