Running on multiple vcf files

[lf-araujo]

I apologize if this is not the correct place for this, as this question is not an issue with the software. Also, thanks for this tool.

I was tasked to calculate a prs, however the data set came in one vcf per chromosome, should I merge all files prior to running the through nimpress?

Thanks

[mpinese]

Thanks, glad you're finding the tool useful!

Yes per-chromosome VCFs should be concatenated prior to running nimpress, using for example bcftools concat. It might be possible to apply nimpress independently to each per-chromosome VCF, then sum the per-chromosome scores later, but this would need some careful attention paid to the imputation process and I'll need to think more about it.

We're planning to do some more dev work on nimpress this year, so if you come across any issues or enhancements during your work with it, please let us know.