_toc.yml

# Table of contents
# Learn more at https://jupyterbook.org/customize/toc.html

format: jb-book
root: index
parts:
  - caption: Module 1 - Introduction
    chapters:
      - file: intro/intro_to_your_genome
        sections:
        - file: intro/genome/structure_DNA
        - file: intro/genome/genome_organization
        - file: intro/genome/central_dogma
        - file: intro/genome/noncoding
        - file: intro/genome/genetic_variation_terminology
        # To add: info on *reference genomes*
      - file: intro/intro_genome_tech
        sections:
        - file: intro/tech/genotype_arrays
        - file: intro/tech/ngs
        - file: intro/tech/long_reads
        - file: intro/tech/tech_summary
      - file: intro/genome_file_formats
        sections:
        - file: intro/formats/vcf
        - file: intro/formats/plink
  - caption: Module 2 - Ancestry
    chapters:
      - file: ancestry/intro_popgen
        sections:
        - file: ancestry/popgen/forces_evolution
        - file: ancestry/popgen/mutations
        - file: ancestry/popgen/drift
        - file: ancestry/popgen/selection
        - file: ancestry/popgen/hwe
        - file: ancestry/popgen/fst
        # TODO: add concept of phase, haplotype
        - file: ancestry/popgen/recombination
        - file: ancestry/popgen/WF-simulations
      - file: ancestry/global_ancestry
        sections:
        - file: ancestry/global/pca_global_ancestry
        - file: ancestry/global/admixture_global_ancestry
      - file: ancestry/relative_finding
        sections:
        - file: ancestry/relfind/ibd
        - file: ancestry/relfind/ibd_pedigree
        - file: ancestry/relfind/ibd_plink
        - file: ancestry/relfind/ibd_segments
#        - file: ancestry/relfind/genetic_genealogy
#      - file: ancestry/admixture
      - file: ancestry/plink_1000G
        sections:
        - file: ancestry/plink1kg/1000G
        - file: ancestry/plink1kg/plink
  - caption: Module 3 - From genotypes to phenotypes
    chapters:
#      - file: complextraits/mendelian
#        sections:
#        - file: complextraits/mendelian/autosomal_recessive
#        - file: complextraits/mendelian/autosomal_dominant
#        - file: complextraits/mendelian/X_linked
#        - file: complextraits/mendelian/penetrance_expressivity
#        - file: complextraits/mendelian/fun_traits
      - file: complextraits/gwas
        sections:
        - file: complextraits/gwas/quantitative_traits
        - file: complextraits/gwas/GWAS-simulations
        - file: complextraits/gwas/confounding
        - file: complextraits/gwas/case_control_traits
        - file: complextraits/gwas/lmms
        - file: complextraits/gwas/power
        # TODO: imputation
      - file: complextraits/heritability
        sections:
        - file: complextraits/heritability/relatives
        - file: complextraits/heritability/lmms-h2
#        - file: complextraits/heritability/ldsc
      - file: complextraits/prs
        sections:
        - file: complextraits/prs/clumping-thresholding
        - file: complextraits/prs/bayesian_prs
#      - file: complextraits/fine-mapping
#        sections:
#        - file: complextraits/fine-mapping/solved-gwas
#        - file: complextraits/fine-mapping/condition_regression
#        - file: complextraits/fine-mapping/bayesian_finemapping
#        - file: complextraits/fine-mapping/trans-ancestry-finemapping
#        - file: complextraits/fine-mapping/coloc
  - caption: Appendix 1 - glossary and notation
    chapters:
      - file: appendix/unix
#      - file: appendix/software
#      - file: appendix/notation
#  - caption: Appendix 2 - review of math+CS concepts
#    chapters:
#      - file: appendix/prob_dists
#      - file: appendix/linear_algebra
#      - file: appendix/hmm
#  - caption: References
#    chapters:
#      - file: references