Purpose: Expression quantitative trait loci (eQTL) identification for a population of 33 healthy canines.
- Genotypes preprocessing
- I was provided with two tsv files including the genotype data from Axiom without their supporting files, therefore I was not able to use bcftools affy2vcf to create the vcf file so I wrote my own function to convert these files to vcf files (See genotyping_code.R)
- All data was then lifted over to canfam4 (code)
- The vcf file was then imputed using Beagle (code)
- Phenotypes preprocessing
- Covariates
- Running tensorQTL