Humble E, Stoffel MA, Dicks K, Ball AD, Gooley RM, Chuven J, Pusey R, Al Remeithi M, Koepfli KP, Pukazhenthi B, Senn H, Ogden R (2023) Conservation management strategy impacts inbreeding and mutation load in scimitar-horned oryx. PNAS. 120, 18. https://doi.org/10.1073/pnas.2210756120.
This repository contains the scripts required for downstream analysis of called genotypes including analysis of ROH analysis, deleterious mutations and recent demography. These scripts include the code to generate the figures in the final paper.
For prior steps including alignment, SNP calling and annotation, please see github repository SHO_reseq_2022.
Relatedness and population structure
1.0_IBD.R
1.1_ngsadmix_out.R
1.2_pcangsd_out.R
ROH analysis
2.0_ROH_plink.R
2.1_ROH_bcftools.R
2.2_ROH_plink_supp
Mutation load analysis
4.0_load_snpeff.R
4.1_load_vep.R
4.2_load_snpeff_supp.R
Ne and fixed loci
5.0_gone.R
6.0_fixed.R
Coverage assessment
0.1_vcf_cov.R
3.0_outgroup_depth.R
6.1_coverage.R
File creation for PLINK
0.0_chrom_map.R
Data files can be generated using scripts from the first part of the pipeline.