How to handle "no call" on SNP imputation results

0

Hi,
i just imputed some SNPs using IMPUTE2, i pruned them and then kept all the haplotypes with probabilities higher than 90% (thresholding was done using Plink1.90)

but what i get is that some SNPs that do not pass the threshold are undefined with the symbol ./. (instead of the normal 0/0, 0/1 or 1/1)

I don't know if what i am doing is right and i need some advice on how to handle them because i would like to keep as much SNPs as possible and not removing samples.

I am new about imputation so any feedback is appreciated.

Thank you.


GWAS


SNP


genotype


Imputation

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