How to convert Haplotypes file to PLINK format data

Question

[bha]

I want to convert Haplotypes data to PLINK format (.map and .ped or binary .fam,.bim, .bed). I wonder, what is best software or R package, can do this easily? Has anybody came across this? Haplotype data is output file from HAPGEN2 (a programme which simulate the sequence data, but unfortunately, there is not a function in this to re-convert back to PLINK).

[Gabriel R.]

is this the output file format: http://www.stats.ox.ac.uk/~marchini/software/gwas/file_format.html ?

[bha]

yes! do you have any sense to convert this to PLINK format?

[Gabriel R.]

could you post a small subset of your file somewhere?

[bha]

The genotype file is exactly in the same format you mentioned in above link, and haplotype is 0s and 1s in standard file. The genytpe look like:

SNP1 rs1 1000 A C 1 0 0 1 0 0
SNP2 rs2 2000 G T 1 0 0 0 1 0
SNP3 rs3 3000 C T 1 0 0 0 1 0
SNP4 rs4 4000 C T 0 1 0 0 1 0
SNP5 rs5 5000 A G 0 1 0 0 0 1

So, at SNP3 the two alleles are C and T so the set of 3 probabilities for each indvidual correspond to the genotypes CC, CT and TT respectively.

Note : columns 2 and 3 (that contain the RS ID and base-pair position of the SNPs are set arbitrarily in this example.

[Gabriel R.]

and you have a sample file as well? are these files simply zipped and not binary?

[bha]

Yes, i do have sample file as well. it's NOT zipped. here are the out files look like: http://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html#top

[Gabriel R.]

and I imagine these probabilities are not just 0 and 1 but can be 0.4 for example? But they have to sum up to 1 I suppose.

[bha]

these probabilities are 0s and 1s. And haplotypes are also in 0s and 1s. what do you suggest?

[Gabriel R.]

but they could potentially be: 0.5 0.5 0? just to be sure.

[bha]

Yes, essentially they are. I have both genotypes, and haplotypes files. My main concern is to convert them to PLINK format, either haplotype or genotypes. Any idea please?

[Gabriel R.]

I can code a module to import them using glactools and export in plink. We currently do not support this format but I could code it.

[bha]

Seems like that GTOOL can do this conversion: http://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#formats

[Gabriel R.]

did you try it? did it work?

[bha]

yes, i think it works well.