Imputation Service FAQs

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General

Array Imputation

General

Can I run the service locally without my data leaving my system?

No, this service is cloud-based and your data must be able to be uploaded to our secure service. Our service is built on top of Terra and is within the same security perimeter, meaning the imputation service is FedRAMP Moderate and approved by the NIH for use with controlled-access data. View Terra's security documentation here.

Array Imputation

How does the service handle allele switches?

Sites with allele switches are dropped because they do not match the reference panel, which is aligned to the hg38 reference. You can check your VCF and fix these sites with the following example tools:

Check reference

bcftools norm --check-ref 

https://samtools.github.io/bcftools/bcftools.html

Determine and fix strand orientation

bcftools +fixref 

https://samtools.github.io/bcftools/howtos/plugin.fixref.html