Hello everyone,

I have 12 singleton WGS samples that I am trying to phase using Shapeit2 using the reference panel method from 1000 genomes. I can successfully run the program and finish with a vcf containing estimated haplotypes for each variant. However, I'm looking for a confidence value on each so I can filter on a strict threshold.

Is there an argument or a simple method that can be used to extract haplotype phasing probability estimates and add them to the vcf file?

Any tips on WGS phasing using shapeit would be great.

Thanks!