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).