Diploid Consensus Sequences
How to separate reads, one for each reference haplotype.

Map all the reads against the reference genome
Use GATK to call SNPs
Use GATK tool [FastaAlternateReferenceMaker][1] to build the alternative reference
You now have the two &quot;haploid references&quot; (quotes needed because you have to take into account that they will not necessarily reflect the exact haplotypic structure, it could be a mix of the two haplotypes)
Align the reads against the two references, and attribute each read to the reference to which they map better. My colleagues developed for a different purpose (detection of Allelic Imbalance) a pipeline that includes the step for determining to which of two references a read belongs. The tool is called [BayesASE][2]

In general you may study all the work that has been done in the field of allelic imbalance and allele specific expression, where this problem has been encountered and solved.
[1]: https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMaker
[2]: https://github.com/McIntyre-Lab/BayesASE