Using a phased reference assembly to phase sample genotypes

I've been trying without success to phase the variants of about 30 samples in a 5Mb non-recombining region. I have a phased genome assembly of the region but so far I have not been successful in using that to inform the phasing of the samples which have been sequenced to high coverage with short reads. Non-reference panel phasing using Beagle 5.2 and Shapeit4 have produced haplotypes that are composed of many small phased blocks which switch phase between them, far to many to manually correct.

I have created a "reference panel" of SNPs of known phase for the region and want to use it to guide the rest of the phasing of the non-"reference panel" SNPs but every method I have found only uses the intersection of the reference panel and the samples for analysis. Is there some technique that I can use to phase the genotypes in the samples? I believe this is a tractable problem since recombination is suppressed in this region so haplotype blocks should be large and contiguous.

• I'm unsure what you mean by "but every method I have found only uses the intersection of the reference panel and the samples for analysis". Do you mean the intersection of SNPs or individuals? In either case, I don't see why that would be an issue. Also, phasing with 30 individuals without a reference panel will give very poor results at best. Nov 3 '21 at 11:41
• Thanks for the reply. My goal was to use the reference panel as a guide to phase the genotypes between the reference panel SNPs. A sort of "reverse imputation". Even though the sample size is small my thought was that since the region in question does not recombine (it is a homozygous lethal inversion) that the nearly complete linkage would make this a workable problem. Nov 3 '21 at 12:23