Plot phasing results

[michal-yoles]

Hi,
I'm new to working with SHAPEIT.
I came across an article titled: "A General Approach for Haplotype Phasing Across the Full Spectrum of Relatedness" (2014) and would like to recreate the same figure as figure 3:

for my own data. I have successfully downloaded and run SHAPEIT5 and obtained a phased VCF. I know there is also an option for a graph output but I'm unsure how to use it for getting this kind of haplotype map.

[RJHFMSTR]

Hi michal-yoles,

This figure can be obtained only if you have a validation set (i.e parent-offspring duos or trios), which allows you to estimate your switch errors. Documentation can be found here: https://odelaneau.github.io/shapeit5/docs/tutorials/ukb_snp_array/#validation-of-your-phasing