Yeah, if anyone is interested in learning more, this is called the phasing problem. For common enough variants, it’s often possible to figure this out by looking at general patterns of co-inheritance if you have a large reference dataset for the population (see: https://www.nature.com/articles/s41588-023-01415-w). Long read sequencing which you mentioned is another approach. But you’re right that these days it would just be cheapest to get the parental genomes (assuming that’s an option).
Yeah, if anyone is interested in learning more, this is called the phasing problem. For common enough variants, it’s often possible to figure this out by looking at general patterns of co-inheritance if you have a large reference dataset for the population (see: https://www.nature.com/articles/s41588-023-01415-w). Long read sequencing which you mentioned is another approach. But you’re right that these days it would just be cheapest to get the parental genomes (assuming that’s an option).