Genotype Imputation for VCF File via API Using R ?

Question

[Ahmed Jaber]

Hello everyone,

I’m working on an imputation of missing SNP genotypes on a vcf file using API in R. I would greatly appreciate your insights and guidance on the issue I’m currently facing.

What I have used:

1. TopMed Imputation Server API I followed the official documentation and was able to successfully connect using a personal API token. However, the server rejected my VCF file because it contains multiple chromosomes. The error message suggests that the file needs to be split by chromosome before submission.

   I am using R (via httr) and not Bash or Python.
   I’d prefer to keep everything in R, if possible.

2. Michigan Imputation Server API As performed in topMed but here it didn't work and faced an error of "404" that meant not found.

Questions

1. Has anyone successfully used TopMed’s imputation server via REST API with multi-chromosome VCFs? If so, what was your solution?

2. What is the best practice for splitting a VCF by chromosome in R? Are there reliable, scriptable functions to automate this?

3. Has anyone used the GDBIG API for genotype imputation? Is this service available via their authentication system, or is it restricted to data access only?

4. Are there other free genotype imputation services with APIs that work well with multi-chromosome VCFs and can be accessed using R?