Question: Genotyped loci changed after imputation by Minimac4
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gravatar for lynnxu1001
5 months ago by
lynnxu10010
lynnxu10010 wrote:

I ran Minimac4 to do imputation on the basis of ~750,000 loci that were genotyped. The reference panel I used was 1000 genome. In the output files, I found that the genotype data at some typed loci changed compared with the input files. For example, Sample 1 was genotyped CC at the locus rs1058164, but in the Minimac output, it is GC at the same locus.

Does this make sense? I used to assume all the typed loci wouldn't be changed by imputation.

Any help is appreciated!

snp imputation minimac4 • 144 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by lynnxu10010
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