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2 hours ago by

Denmark

Hi,

I wish to compare the performance of two genotyping chips for phasing and imputation protocols on a dataset. To do this, I have masked a small set of 10k SNPs in the dataset from each chip prior to pre-phasing and phased each dataset using three different tools. Now due to resource constraints on disk space, I wish to only impute the 10k masked SNPs to evaluate the performance of each of my protocols.

I'd like to know if it is possible to do this using Beagle5.1 as there doesn't appear to be a straight forward option to selectively impute markers from the manual.

Cheers!

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Vivek2.3k



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