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!
We had a related discussion in a prior thread by OP: Software to separate reads from different individuals
Do you have genotype (or independent sequence) data available for the mother?
This is related to that other question but for now, the only thing I'm interested in is separating the three unique chromosomes, without assigning them to mother or fetus. The result would be unique reads from one person, unique reads for the other, and shared reads.