Question: How to determine the haplotypes using Beagle
gravatar for akang
4.0 years ago by
akang90 wrote:

I have two datasets one has genotype data for 30 SNPs and one has genotype data for 29 SNPs.I want to impute for the missing SNP and also want to determine the haplotype using these SNPs. This is how i am running the imputation in beagle

beagle.jar phased=file.phased unphased=test.unphased markers=markers missing=0 out=Result.

I get the imputed file as the result of this command but how do I get haplotype file? Ill appreciate any help.

beagle snp haplotype • 2.4k views
ADD COMMENTlink written 4.0 years ago by akang90
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