Question: Phasing And Imputation Using A Combination Of Pedigrees And Population Data
gravatar for Lrk
8.5 years ago by
Lrk40 wrote:

Through 23andMe, I have SNP genotypes from family members spanning three generations, incl. one parent and a sibling of the missing parent, multiple siblings in the middle generation, one child in the the third generation and the child's other parent, and some cousins. Some of these have around 500,000 markers, and some of them have around a million.

I want to phase these and infer the genotypes of the missing parent, and also use imputation to bring each individual as close to the million snps as reliably possible, using a combination of information contained within the pedigree and also data from sources like the 1000 Genomes Project. Do you have any advice on how to accomplish this or which programs if any would work?

imputation genomics snp • 3.0k views
ADD COMMENTlink written 8.5 years ago by Lrk40
gravatar for Michael Dondrup
8.5 years ago by
Bergen, Norway
Michael Dondrup47k wrote:

List of tools and documentation (there are more ofc, could someone link review papers on imputation and phasing?):

For phasing: e.g. fastPhase

For imputation:

ADD COMMENTlink written 8.5 years ago by Michael Dondrup47k
gravatar for Zev.Kronenberg
8.4 years ago by
United States
Zev.Kronenberg11k wrote:

I like BEAGLE it is fast and you get Identity by decent from it as well. BEAGLE LINK

I would be careful about how much data you are missing. I don't allow a loci to have more than 5% missing data for all individuals.

ADD COMMENTlink written 8.4 years ago by Zev.Kronenberg11k
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