hifiasm
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Obtaining phase sets
I am using the two haplotype assemblies of hifiasm
(fasta
files extracted from the*hap*.p_ctg.gfa
files). Is there a way to obtain the phase sets/phasing blocks used in construction of these haplotypes? To be concrete, I would like to know, for each two positions along the same haplotype, if there was evidence in the assembly graph to support those two positions coming from the same parental chromosome; or were they arbitrarily put together in the same gfa
.
Are distinct phased contigs within each gfa
file the same as a consistent phase set?
Thanks for creating this great software!