The LOWCONF filter indicates that the variant was not imputed with high confidence. More precisely, it means that none of the posterior probabilities for the possible genotypes (0, 1 , or 2) for that variant exceeded 0.9.
The LOWCONF filter indicates that the variant was not imputed with high confidence. More precisely, it means that none of the posterior probabilities for the possible genotypes (0, 1 , or 2) for that variant exceeded 0.9.