Figure 1 - The pipeline for the creation of per Single Nucleotide Polymorphism (SNP) pink pigeon Combined Annotation Dependent Depletion (ppCADD) scores from raw reads of individual pink pigeons.The Snakemake pipeline uses as input the sequencing reads of the subject individuals, the subject species reference genome, and the CADD scores and reference genome of a model species (i.e., chicken, chCADD scores and the Galgal6 reference genome ). The pipeline is separated into six sections, corresponding to sections of the pipeline (https://github.com/saspeak/LoadLift). (1) (Yellow) Extraction of UCEs from the reference genome using Phyluce. (2)(Dark Blue) Mapping the sequencing reads for individuals to the reference genome indicating two parallel approaches for 10X chromium read data (used in this paper) and for Illumina read data. (3)(Light Blue) Variant calling for SNPs within the UCEs. (4)(Light grey) Creation of a chain file for the liftover of annotation from the chicken genome. (5) (Dark Grey) chCADD scores conversion to pink pigeon (subject species) annotation. (6)(Green) Intersection of BED files and UCE sites to output per site ppCADD (subject species) scores (Red).