Imputing specific SNPs using Beagle5.1
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4.4 years ago
Vivek ★ 2.7k

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!

imputation beagle • 1.6k views
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Can't tell for sure, but I think impute2 has an option of only impute missing - "fill in", beagle should have something similar, too. If not another solution would be to trim down the panel to match your SNP list.

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I tried to subset the reference but beagle's default mode is to impute in 40 mb chunks with a 4 mb overlap so if I were to try and replicate that for my 10k masked SNPs, it becomes cumbersome enough to do whole genome imputation.

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