Not designed for ploidy != 2

[sdtemple]

This design is due to the pipeline dependence on hap-ibd.jar and ibd-ends.jar and 2-ploidy VCF file with |. The estimation procedure can handle any ploidy.

[sdtemple]

You can refer to the workflow/scan/rules and workflow/roi/rules as the blueprint to implement the methods. The scripts for each rule are defined there. You would need a method to detect IBD segments for ploidy != 2. You may need to change the functions in script rank.py that bring in and manipulate the VCF file.

Overall, the paper puts forth the conceptual framework of the methods. These implementations in bash and python are specific to ploidy = 2.

Furthermore, it is possible in some rules/ or scripts/ that I have hard-coded diploidy.