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Michigan Imputation Server - typed-only sites?

HI all, I have been trying to carry out imputation on some datasets on the Michigan Imputation Server, and have been getting SNPs excluded due to being "Typed only sites".

Could anyone explain what this means? I am looking to standardize the number of SNPs across my inputs, so I would like to understand this before I exclude them. Thanks!

imputation snp genotyping michigan vcf
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updated by jpeijia • jpeijia • written by Volka Volka

Imputation is done in chunks, and your SNPs do not fall into those chunked regions. Maybe your build is different?

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written by zx8754 zx8754

So these typed only sites could actually be sites that are on a chunk that got dropped because of poor overlap with the reference?

Also could be sites that were on a chunk that was not dropped but the site had no match with the reference?

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written by curious curious

Same problem I met. Cannot solve it so far.

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written by jpeijia • jpeijia

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