Hi there,
I have diploid calls from long reads HiFi for a sample on both his haplotypes/assemblies (I'm working with humans, so I have only hap1 and hap2). Is there a way to correctly merge these two files based on a single reference?
The idea is to test and benchmark the effect of mapping to the genome of origin for the sample against any linear reference, which in theory should have better performance. I'm open to other suggestions if this won't be possible; for instance, mapping to the "most complete" between the two haplotypes then combine the two VCF files to prevent issues with mismatches in reference calls.
This would be still better than mapping to a different reference but won't capture variants inherent the other haplotype. Let me know what you think, thanks in advance!
