Defining Local Haplotype Variants for Use in Trait Association
and Trait Prediction Analyses
Description
A local haplotyping tool for use in trait association and trait prediction analyses pipelines.
'HaploVar' enables users take single nucleotide polymorphisms (SNPs) (in VCF
format) and a linkage disequilibrium (LD) matrix, calculate local haplotypes and format the
output to be compatible with a wide range of trait association and trait prediction tools.
The local haplotypes are calculated from the LD matrix using a clustering algorithm called
density-based spatial clustering of applications with noise ('DBSCAN') (Ester et al., 1996)
.