Genome-wide association testing with CNV data

[alimanfoo]

Umbrella issue to review and explore approaches to genome-wide association testing using CNV data, specifically for discovery of insecticide resistance genes and variants. The goal being to propose some functions to implement in malariagen_data.

Some starting points:

• Look at GWAS methods used in Lucas et al. 2023
• Look at GWAS methods used in Lucas et al. 2024

N.B., suggest scoping this issue to just use of CNV data. See separate issues for association testing using SNP (#679) and haplotype (#684) data.

[alimanfoo]

Does Lucas et al. (2024) do a GWAS with CNV data, or does it just test specific CNVs within regions under selection for association with phenotype?