Question: Michigan Imputation Server removed low call rate SNPs
0
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
duplicates
indels
monomorphic sites
allele mismatch between reference panel and uploaded data
SNP call rate < 90%

Thanks.

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