A generic hidden Markov model for multi-parent populations

This repository contains the source for the paper

Broman KW (2022) A generic hidden Markov model for multi-parent populations. G3 (Bethesda) 12:jkab396

• gen_hmm.Rnw - source document (LaTeX + knitr)
• gen_hmm_bib - BibTex bibliography
• DOapp/ - application to Diversity Outbred mice - do_analysis.html
• CCapp/ - application to Collaborative Cross mice - cc_analysis.html
• Makefile - GNU Make file

Required R packages

• R/qtl2
• qtl2convert
• qtl2fst
• broman
• data.table
• readxl
• here

License

The content in this repository is licensed under CC BY 4.0.