How To Compute Haplotype Blocks?

Question

[Juan Duran]

Hello,

I'm a computer science student, I'm developing my thesis degree application and I'm working with LD Plotters.

I need to know how to compute haplotype blocks to develop the LD Plotter, building from a PED File, and how to translate this http://hapmap.ncbi.nlm.nih.gov/cgi-perl/phased?chr=chr3&pop=JC&start=2000000&stop=2100000&ds=pIII&out=txt&filter=cons+jc (a query to hapmap db) to a PED File, for then buildign a LD Plot.

About the PEDFile I know the first 6 columns, but the rest I have no idea.

Where I can I find information about that?

I'm urgently needing it.

Thanks in advance.

Answer 1

[Larry_Parnell]

Juan,

The 7th and onward rows in the link you provide give rs accession for individual SNPs within the region you are examining. The number following each SNP ID (rs12345, e.g.) is the position in the genome.

Further down, you have "phased haplotypes." These are identified by the identifiers for those individuals who particpated in the HapMap project. Thus, NA18524 signifies an individual. The "_c1" and "_c2" suffixes signify copy 1 and copy 2 of the phased haplotypes. Recall that each individual has two copies of a each chromosome - one from mom and one from dad.

From those phased haplotypes you should be able to progress with your project.

You may find more info of use at the HapMap tutorial page.

[Juan Duran]

Thanks for your answer.

There's no information about how to compute haplotypes blocks on the HapMap tutorial page, it's a tutorial about how to use the web interface of the HapMap querier.

I understood what you told me and I started my development on that, now I "parse" [?]this[?] on [?]this other thing[?].

I still have no idea about how to do the math to get the LOD, R2, D' for example.

[Juan Duran]

Thanks for your answer.

There's no information about how to compute haplotypes blocks on the HapMap tutorial page, it's a tutorial about how to use the web interface of the HapMap querier.

I understood what you told me and I started my development on that, now I "parse" http://hapmap.ncbi.nlm.nih.gov/cgi-perl/phased?chr=chr3&pop=CEU&start=200000&stop=250000&ds=pIII&out=txt&filter=cons to http://bioinf.cs.ipm.ir/gpmap/examples/sample.ped with what you told me.

I still have no idea about how to do the math to calculate the LOD, R2, D' for example.

Do I have to do something with allele freq?

[Juan Duran]

I have no biology background.

What do you recommend me to read?

Thank you.

[Juan Duran]

I have no deep biology background. What do you recommend me to read? Thank you.

[Larry_Parnell]

I cannot tell you how to calculate the r^2 values. Sorry, but that is not something I have done without the use of a tool like Paul de Bakker's Tagger program. See de Bakker et al., Nature Genetics Advance Online Publication 23 October 2005 doi:10.1038/ng1669) visit tagger website. Or try Haploview - from HapMap website: For performing in depth LD and Haplotype analysis of genotype data, install Haploview in your local machine. Haploview (ver 4.1) is currently available for download.

[Juan Duran]

Ok! Thank you very much!

[Radhouane Aniba]

I think you can find information you are looking for just here http://www.sph.umich.edu/csg/abecasis/class/666.03.pdf