Question: Haplotype construction based on SNPs with haploview
1
gravatar for Ripeapple
6.3 years ago by
Ripeapple40
United States
Ripeapple40 wrote:

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!!!

haploview snp • 5.4k views
ADD COMMENTlink modified 6.3 years ago by viavialin70 • written 6.3 years ago by Ripeapple40
0
gravatar for Floris Brenk
6.3 years ago by
Floris Brenk970
USA
Floris Brenk970 wrote:

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

http://www.broadinstitute.org/science/programs/medical-and-population-genetics/haploview/input-file-formats-0

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

 

ADD COMMENTlink written 6.3 years ago by Floris Brenk970

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

 

 

ADD REPLYlink written 6.3 years ago by Ripeapple40
0
gravatar for viavialin
6.3 years ago by
viavialin70
Canada
viavialin70 wrote:

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!
ADD COMMENTlink written 6.3 years ago by viavialin70

Thank you so much, The format works,

ADD REPLYlink written 6.3 years ago by Ripeapple40
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