Obtaining phased haplotype data

Question

[kshitijtayal]

Hi all,

I am doing my research on Haplotype inferencing and i need my hand on some real phased haplotypes.

I understanding that haplotype data is available at international Hap-Map project but the problem is that it comes from a tool called Shapeit.

Can anybody point me to any resource where i can get actual sequenced phased data about haplotype of different individual rather than data coming out of any model or simulation tool.

Thanks in advance.

Answer 1

[Fabio Marroni]

There are several options.

1. In this paper they used Hi-C to reconstruct (nearly) chromosome-long haplotypes on molecular data. However, I am afraid that only one individual was haplotyped.

2. If you just need one (or few individuals) you can look on the internet for haplotypes assembled with PacBio technology.

3. You can use trio data from the 1000 genome and get reasonably accurate haplotype reconstruction

4. The easiest option is to only analyze the X chromosomes of female daughters from trio data. You have the X paternal haplotype easily (since males are XY) and from it you subtract the other allele and you get the maternal X haplotype.