Dataset: Combined Annotation Dependent Depletion (CADD) scores for turkey and chicken

This dataset contains genome-wide CADD (Combined Annotation Dependent Depletion) scores for chicken and turkey, generated as part of research aimed at predicting the deleteriousness of genetic variants in non-model species. The objective of the study was to develop and apply a generic, species-agnostic pipeline that computes CADD scores using only a high-quality reference genome, corresponding gene annotation, and a multi-species alignment (MSA) to infer ancestral sequences. The research involved computational methods rather than experimental sample collection; genomic reference assemblies, available functional annotations, and an evolutionary MSA were used as input features to train a machine learning model that assigns PHRED-like CADD scores to all possible single nucleotide variants across the genome. The resulting data consist of chromosome-wise tab-delimited files containing CADD scores for chicken (<code>chr{chr}.tsv.gz</code>) and turkey (<code>Turkey_chr{chr}.tsv.gz</code>), which can be used for comparative genomics, evolutionary analyses, and prioritization of candidate variants in genomic and breeding studies. The work is described in the publication <em>“A generic pipeline for CADD Score generation: chickenCADD and turkeyCADD”</em>, accepted in <em>G3</em>.