Question about Haplotype scaffold

[tgong1]

Hi,

Thank you for developing and maintaining this useful tool. We got a question about the haplotype scaffold can be used.

For our samples, we got a subset of variants with high-quality haplotypes, but not chromosome-length. This means this set of genotype data have multiple haplotype blocks (with PS tag) in VCF. If this set of genotype data is used as haplotype scaffold, does shapeit5 only assume chromosome-length haplotype (ignore PS tag) or it will somehow consider the existence of multiple haplotype blocks based on the PS tags ?

Thank you for the help!