Question: Obtaining phased haplotype data
gravatar for kshitijtayal
3.2 years ago by
kshitijtayal30 wrote:

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.

sequencing haplotype next-gen • 1.2k views
ADD COMMENTlink modified 7 months ago by RamRS21k • written 3.2 years ago by kshitijtayal30
gravatar for Fabio Marroni
3.2 years ago by
Fabio Marroni2.1k
Fabio Marroni2.1k wrote:

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.

ADD COMMENTlink modified 7 months ago by RamRS21k • written 3.2 years ago by Fabio Marroni2.1k
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