Genotyped SNPs were lost after michigan imputation server imputation and phasing

Question

[Shicheng Guo]

Hi All,

I run a imputation and phasing with 'michigan imputation server' for exom-beadchip array data and I found some of genotyped SNPs in the exom-chip were lost in the output file. Is it common or I made some mistake in the option selection or others?

Thanks.

[Kevin Blighe]

Check the output logs. The Michigan Imputation Server likely outputs a report of what was excluded, and why.