Hi everyone,

I recently phased my data using Shapeit2, and I am wondering how I would check the quality of the phasing process on my data.

I've read solutions only that can do this when you already have a vcf file that you know is correctly phased, such as with the vcftools --diff-switch-error option, but I do not have such a file. Just my original, unphased vcf, and my newly phased vcf.

How might I determine whether the shapeit output is acceptable?

Thanks!