Assessing ancestry of North American honey bees (Apis mellifera) through low-pass whole-genome sequencing

Important Files

• ahb_pipeline_v2.sh
  • full bash script to run ancestry analysis and PCA using imputed data
• unimpt.sh
  • version of above taking only observed genotypes (uses no imputation)
• n_mitotype.sh
  • full bash script to run mitotyping analysis
• aimIa_v2.R
  • custom R script to caluclate site informativeness for ancestry
• ahb_analysis.R
  • analyses included in publication, including logistic regression, PCA, and ancestry figures
• corr_concordance.cpp
  • This C++ program used to estimate correlation and concordance rate between imputed and observed genotype for a large-dimenssional dataset. The code will generate a dataframe of concordance rate and imputation accuracy.
• recombRate.R
  • custom R script to calculate recombination rate