Repository for notes and config files for constructing a Zea Mays practical haplotype graph using 25 NAM founders and 11 Zea Synthetic lines.
- The pipeline bash file contains commands and comments corresponding to all steps necessary to create, fill, and impute the PHG through singularity on our systems.
- The PHG workflow word file includes documentation of older and miscelaneous testing commands. As well as a list of common errors and how to address them.
- Each config file corresponds to a specific command stores within the pipeline bash file, with each parameter annotated by me.
Please contact tk9066 @ princeton.edu for questions.