I am a beginner in this field and trying to reveal de novo variants in a trio vcf file (Parents-unaffected, child-affected). First, I used PhaseByTransmission tool and then formed a new .vcf file consisting of only unphased variants ("/" instead of "|"). To my knowledge, de novo variants cannot be phased by the tool because they are not transmitted from the parents.
Here is my question, what are the next steps to identify more accurate de novo variants? Because there is almost 500k unphased variants in the final vcf file and I think it is not possible that all the candidates are true de novo variants.
Thank you so much for your helps!