Question: Haplotypes; phasing, positve seletion and estimating age
gravatar for Floris Brenk
4.3 years ago by
Floris Brenk970
Floris Brenk970 wrote:

Hi all,

I have some (about 500 samples) NGS resequencing data (>100x coverage) of a few regions (Illumina reads 2x100bp). Now I want to do several things: 1. Haplotype phasing (-> assign haplotypes and which variants are on which haplotype etc.) 2. See whether there has been a positive selection for haplotypes during human evolution 3. Estimate the age of the identified haplotypes

Does anyone has experience with these analyses and can point me to which software I should use?

resequencing haplotypes • 1.3k views
ADD COMMENTlink modified 4.3 years ago by Giovanni M Dall'Olio27k • written 4.3 years ago by Floris Brenk970
gravatar for Giovanni M Dall'Olio
4.3 years ago by
London, UK
Giovanni M Dall'Olio27k wrote:

For the imputation you may use the Haplotype Reference Consortium Resources:

Because of privacy restrictions you cannot access the data used for the imputation, but the data used is from 64K individuals, much more than what you can expect to collect by yourself.

For the selection you may calculate iHS to identify recent selective sweeps, and XP-EHH to identify sweeps occurred in a population but not in other.

In general you get better results if you ask only a single question at a time, otherwise it is difficult to answer you in details.

ADD COMMENTlink written 4.3 years ago by Giovanni M Dall'Olio27k
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