GLIMPSE imputation result
Hi, there I'm new in imputation and phasing. I'm using this tutorial for learning imputation. In my understanding, we should get more SNPs(imputed from the reference panel) after imputation but in reality(running the script from this tutorial), we are getting the same amount of SNPs as the input. What am I missing here? Can anyone explain me?
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Shafayet •
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crossposted w/ answer here https://bioinformatics.stackexchange.com/questions/18270/interpreting-imputation-result-from-glimpse
used --impute-reference-only-variants option. But, doesn't change the result. Do I need to pass any argument like --impute-reference-only-variants <arg>. Can anyone give an example?