This project directory contains all scripts for The impact of identity-by-descent on fitness and disease in dogs (Mooney, Yohannes, and Lohmueller 2021).

All the Rscripts used are in the folder titled: Local Rscripts and subdirectories are labelled by the analysis
-The OMIA files are in the OMIA directory, file name: processedCausalVarsOMIA.txt
-The AKC files are in the AKC directory, file name: AKC_breedPopularity_1926thru2005.txt
-The ROH files are in the ROH directory, file name: TrueROH_propCoveredwithin1SDMean_allChroms_mergedFile_Cornell_allChroms_vcfToolsROH_rmROHlessThan50snps_HaywardDataOnly.txt
-The locations of the genes with at least one exon without a ROH are in the InbreedingDepAnalyses folder in the sub-directory VettingResults, file name: SupplementaryFileFormat_ExonRegion_NonOverlapsROH_cornellData.bed

The plink files used that contain the merged data sets from Fitak and Hayward are in: MergeFitkakAndCornell directory in the zipped sub directory called FinalFiles.tar.bz2
-In the sub directory I include a readme and scripts for how files were created.