Does Beagle use VCF information such as the "GQ" value, depth, or similar?

Question

[a5864557]

Does Beagle 5.4 take VCF information such as the "GQ" value, depth, or similar into account which producing an imputed genome?

Answer 1

[4galaxy77]

No, it just uses the genotypes. Older versions take into account genotype likelihoods, but that's not been since 4.1

[a5864557]

Interesting. I wonder why they dropped it.