Equine_late_greying

Data and code relating to "An intronic copy number variation in Syntaxin 17 determines speed of greying and melanoma incidence in Grey horses"

PLINK was run using genotypes from horses displaying Grey and Late Grey phenotypes with the following command:

plink --file Grey --pheno Grey.pheno --pheno-name Greying --model --fisher --allow-no-sex --horse --out assoc_model_fisher.out

Results from this association test (Dominance model) can be found in the files:

LateGrey_vs_grey_PLINK_dominance_gwas.results.chr1-10.txt.gz LateGrey_vs_grey_PLINK_dominance_gwas.results.chr11-20.txt.gz LateGrey_vs_grey_PLINK_dominance_gwas.results.chr21-and-above.txt.gz

The python script WinNuclDivmPileup500kb.py was used to generate nucleotide diversity estimates along the genome from nanopore data of a G2/G2 horse.