cLDLA

cLDLA implements a Nextflow workflow that performs combined linkage disequilibrium and linkage analysis (cLDLA) to identify the genetic basis of complex traits.

Key Features:

• Combined linkage disequilibrium and linkage analysis (cLDLA): The workflow implements the statistical approach first proposed by Meuwissen and colleagues in 2002, which is robust against population stratification and family structure and requires relatively lower sample size compared to genome-wide association study design.
• Input processing: The workflow accepts a VCF file and phenotype file as inputs and implements all downstream processing required for cLDLA, including complex computation processing and intermediary file conversion steps.
• SNP-based heritability estimation: The workflow includes a separate workflow to estimate SNP-based heritability.
• Result visualization: The workflow features interactive visualization of results.

Scientific Applications:

• Quantitative trait loci mapping: cLDLA identifies loci associated with measurable traits influenced by several polymorphic genes and environmental conditions.
• Livestock genetics: The underlying cLDLA approach has been used to identify the genetic basis of polled condition in cattle and tail length in sheep.
• Complex trait analysis: cLDLA identifies the relationship between polymorphism segregating in a population and phenotypic differences of a trait observed between individuals.

Methodology:

The workflow is implemented in Nextflow and requires a VCF file and phenotype file as input. The sources do not provide further explicit detail on specific computational steps beyond downstream processing, intermediary file conversion, SNP-based heritability estimation, and interactive visualization of results.