Question: Michigan Imputation Server removed low call rate SNPs
gravatar for Shicheng Guo
15 months ago by
Shicheng Guo8.5k
Shicheng Guo8.5k wrote:

Hi All,

I notice Michigan Imputation Server removed all the low call rate SNPs (rate<90%??) before the imputation and phasing. Is there any way to remove this criterion?

contains invalid alleles
monomorphic sites
allele mismatch between reference panel and uploaded data
SNP call rate < 90%


ADD COMMENTlink modified 13 months ago by Biostar ♦♦ 20 • written 15 months ago by Shicheng Guo8.5k
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