I have a question about what I first thought would be a trivial task. I would like to resolve the haplotypes of a non-model (diploid) species. I have a genome assembly, and a bam file where the reads (that were used for genome assembly) are mapped. The genotype of the mapped reads is thus the same as the "reference" genome, I just want to properly resolve the two haplotypes.
Since the genome assembly is by definition a chimera of both haplotypes I cannot just take the assembly as a reference and call SNPs (which I would do with haplotypeCaller from GATK). I tried using samtools phase (which sounded like the perfect solution for the problem) but I have a hard time interpreting the output file so I am not even sure if this is what I'm looking for, especially since some SNPs are clearly missed in the output and some seem to be sorted incorrectly.
I'm unlikely the first person to try to do this (even though I cannot find any similar questions on BioStars), so my question is - which tools do you use to phase/resolve haplotypes?