Michigan Imputation Server removed low call rate SNPs

Question

[Shicheng Guo]

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
duplicates
indels
monomorphic sites
allele mismatch between reference panel and uploaded data
SNP call rate < 90%

Thanks.