Hello all

I'm working with blood samples with mixed DNA from mother and fetus and sequencing with Nanopore (not cell free DNA, so long reads). I need to phase this mixture to separate the three haplotypes, one unique from the mother, one unique from the fetus (which was inherited from their parent) and a shared one between mother and fetus (the one inherited from the mother by the fetus). The final results I'm looking for are a bam file with the reads from the unique chromosome of the mother, another with the reads from the unique chromosome of the child and another with the reads from the shared chromosome. In theory I will have sufficient depth in the region I'm interested on for phasing. I don't have a lot of experience in bioinformatics so I'm not sure how to approach this, if someone could give me some advice I will highly appreciate it.

Thank you!