Closed sdtemple closed 3 months ago
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.
This design is due to the pipeline dependence on
hap-ibd.jar
andibd-ends.jar
and 2-ploidy VCF file with|
. The estimation procedure can handle any ploidy.