Question: Reconstruction Of Haplotypes From The Genotypes On Snps
12
gravatar for Pierre
9.0 years ago by
Pierre480
Spain
Pierre480 wrote:

Hello everybody,

I need an advice concerning the reconstruction of haplotypes from the genotypes on SNPs for different sets of individuals. Here is the situation:

I am using fastPHASE. I have 2 different levels of analysis: - first level, the global level: looking at a set of 940 individuals - second level, the regional level: looking at subsets of these 940 individuals. Then I have 100 individuals for Africa, 64 for AMerica and so on.

I have filtered the SNPs for MAF>=0.05 and known genotype for >= 90% of the individuals for each region and for the global level (giving different subsets of SNPs). So I am wondering if I have to run fastPHASE for each region or if, for each region I can extract from the phased data obtained for the Global, the haplotypes for my sub sets of SNPs and individuals. This is possible because intrinsically at the Global level the subset of SNPs does contain all the SNPs from each subset for each population.

Since fastPHASE is very time-demanding, extracting from the phased data obtained for the Global level will allow me to save A LOT OF TIME: I wouldn't run fastPHASE for the 7 regions. On the other hand I guess that fastPHASE do not run the same way if we have intermediate SNPs (extracting form phased haplotypes obtained at the Global level) and if not (running fastPHASE for each region). How important will you expect the difference to be?

I do not know if it is clear enough and if you have a defenitive answer for this. Anyway thanks for your help!

cheers Pierre

haplotype genotyping • 5.9k views
ADD COMMENTlink modified 7.7 years ago by Eric Normandeau10k • written 9.0 years ago by Pierre480

This is an interesting question. Can you add links for the software you are using, please?

ADD REPLYlink written 9.0 years ago by Michael Dondrup45k

Here it is: http://stephenslab.uchicago.edu/software.html You have two quite similar software: PHASE and fastPHASE. The algorithm is a bit different in the second one which makes it faster although more approximative.

ADD REPLYlink written 9.0 years ago by Pierre480

Can you provide some more information? I think this is a very interesting toppic, but also a very complex one. I would like to know about the input data for the software. I assume it takes the genotypes of each person as a vector like f.e. (C,C/A,T,T/A), is that correct? Does the software recognize the sub-groups at all if you give the whole population data? I mean, can you specify sub-groups at all?

Did you contact the author already?

ADD REPLYlink written 9.0 years ago by Michael Dondrup45k

Oooops sorry I haven't been alerted that there was a comment to answer. The inpout data is as following: a genotypefile: for each individual 2 vector of A/T/G/C, one per chromosome a (facultative) population file: where you precise the population code for each individual. And that's it! So I do not know if you know the HGDP panel: I have 39 populations in 7 regions. I did precise the appartenance to one of 39 populations for each individual. Do you need more precision?

ADD REPLYlink written 9.0 years ago by Pierre480
2
gravatar for Eric Normandeau
9.0 years ago by
Quebec, Canada
Eric Normandeau10k wrote:

Hi Pierre,

I am sorry that I cannot answer precisely to your question since I am not familiar with fastPHASE. However, here is a website with some information about HaploBlock, which claims to be able to do haplotype construction. The site also has a section with additional information and links, including a link to the huge HapMap project and other software of interest.

Hope it can be of use. I'll ask around the lab tomorrow to see if anybody is more acquainted with haplotype construction than I am.

Cheers!

ADD COMMENTlink modified 8.9 years ago • written 9.0 years ago by Eric Normandeau10k
1
gravatar for Khader Shameer
8.9 years ago by
Manhattan, NY
Khader Shameer18k wrote:

Have you tried Haploview ? I can see a tab for HapMap PHASE on Haploview 4.2. http://www.broadinstitute.org/haploview/haploview. And google fetch me this link with a set of haplotyping tools http://www.soph.uab.edu/ssg/linkage/haplotyping.

ADD COMMENTlink written 8.9 years ago by Khader Shameer18k

I'm not looking for a method for haplotype reconstruction...

ADD REPLYlink written 8.9 years ago by Pierre480

Oops. Sorry about that.

ADD REPLYlink written 8.9 years ago by Khader Shameer18k

no problem! It is just that I'm sure that is not a matter of software.

ADD REPLYlink written 8.9 years ago by Pierre480
1
gravatar for Pierre
8.9 years ago by
Pierre480
Spain
Pierre480 wrote:

But maybe both of you think that using the methods you speak about (haploview and HaploBlock) , I would not have to phase my genotypes at all levels and I can use the phased genotypes at the highest level (GLOBAL) to extract the phased genotypes at lower levels (for less snps and individuals). Maybe it works for these methods (I know the software haploview to measure LD but I have no knowledge of both the methods for haplotype reconstruction)

Regards!

ADD COMMENTlink written 8.9 years ago by Pierre480
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