Imputation from targeted DNA sequencing?

metheuse · 06-28-2020, 01:19 PM

We have done genotyping from targeted DNA sequencing of 600 related human samples. The targeted regions are mainly the exons of several hundred imprinted genes and the total size of the panel is 4Mb. About 200 samples were in trios and we were able to phase their variants. We are wondering if we could use these genotyping and phasing data to impute the SNPs beyond the targeted regions, e.g. several Kb or Mb upstream/downstream of the genes we targeted in the panel. All the sequenced samples came from a small local population so it's expected that they share many common haplotypes. Will this help imputation? If it's feasible, which pipeline/tools should be used? Thanks.

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06-28-2020, 01:19 PM	#1
metheuse Member Location: US Join Date: Jan 2013 Posts: 78	Imputation from targeted DNA sequencing? We have done genotyping from targeted DNA sequencing of 600 related human samples. The targeted regions are mainly the exons of several hundred imprinted genes and the total size of the panel is 4Mb. About 200 samples were in trios and we were able to phase their variants. We are wondering if we could use these genotyping and phasing data to impute the SNPs beyond the targeted regions, e.g. several Kb or Mb upstream/downstream of the genes we targeted in the panel. All the sequenced samples came from a small local population so it's expected that they share many common haplotypes. Will this help imputation? If it's feasible, which pipeline/tools should be used? Thanks.