How to obtain the alignment of two hap for an individual

[xuxingyubio]

I hope this message finds you well. I am currently working with Cactus and have a specific question regarding the analysis of differences between two haplotypes. Specifically, I am interested in identifying the differences between the two haplotypes in complex regions, such as the MHC region. Ideally, I would like to obtain base-by-base alignments between alleles, similar to what is available in the IMGT database.

Could you please advise on the best approach to achieve this using Cactus, or recommend any tools or methods that would allow me to obtain such detailed comparisons?

[glennhickey]

I guess you'd want to use cactus-pangenome since it'll give you the output in graph and vcf format which may be easier to use than the HAL/MAF from progressive cactus.

[xuxingyubio]

Thank you for your reply. I plan to use minigraph-cactus but would like to use a haplotype assembly from a single individual as the reference. However, this assembly is relatively fragmented. If I include more complete assemblies such as CHM13v2 or GRCh38 alongside my fragmented assembly, will this affect the construction of the graph?

[glennhickey]

minigraph-cactus expects a chromosome-level reference assembly so you're probably better off using one. it should only take a few minutes to run, so you can try both ways if you want.