Output SNP data after imputation
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Entering edit mode
7 months ago
nbrad • 0

Hey,

I am only getting started with learning how to process genomics data, therefore I need some help making sense of the output of the Michigan imputation server. So, I imputated my genotypes, run QC and then extracted the dosage matrix, however now the output looks like this containing a variety of numbers ranging from 0 to 2:

id Sam1 Sam2 Sam3 Sam4

rs12238997 0.013 0.479 0.005 0.002

rs12029736 0.603 0.96 1.629 0.95

rs4951859 1.741 0.911 1.797 1.814

while I was expecting something like AA AC CC?

Maybe it has something to do with the reference?

Thank you in advance for your time!

genomic genomics snps snp imputation • 220 views
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Entering edit mode

Dosage is a number (the expected number of copies of the alternate allele), so it makes sense in your output it is a number rather than AA / AC / whatever.

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