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14 months ago
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Does Beagle 5.4 take VCF information such as the "GQ" value, depth, or similar into account which producing an imputed genome?
Does Beagle 5.4 take VCF information such as the "GQ" value, depth, or similar into account which producing an imputed genome?
No, it just uses the genotypes. Older versions take into account genotype likelihoods, but that's not been since 4.1
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Interesting. I wonder why they dropped it.