varLD: A program for quantifying variation in linkage disequilibrium patterns between populations
This program can be used to perform inter-population comparison of regional patterns of linkage disequilibrium (LD), and quantifies which genomic regions carry dissimilar patterns of LD across the populations compared.
Regions identified by this algorithm have been reported to concur with known genomic areas carrying different haplotypes, candidate signals of positive natural selection, and in regions known to possess structural variants and copy number differences.
A zipped file containing the main software and its required java libraries can be downloaded varld-1.0-20100307.tar.gz
Please refer to the README for program instructions.
The following files are provided as an example dataset for input to varLD.
These files comprises of the genotype data from two SGVP populations: CHS and INS, on chromosome 16, positions 29Mb to 33Mb.
Example: java -jar rgenetics-1.0.jar -p VarLD chs-chr16-29mb_33mb.txt ins-chr16-29mb_33mb.txt
Plotting and interpretation of varLD results
The varLD program provides as default, output of the raw varLD scores. We thus standardized the scores from the genome-wide assessment to have a zero mean and a variance of one. This standardized score allows a convenient way to display the varLD scores from the assessments involving multiple pairs of populations. The varLD metric looks for regions carrying regional patterns of LD variation that are more differentiated between two populations, compared to the rest of the genome, and this is the basis on which we interpret the varLD scores. We thus advocate interpreting each specific varLD score against the genome-wide distribution, whether it’s in the top 0.01 percentile, or whether it is in the top 30th percentile.
The following R scripts and example standardized varLD scores around the VKORC1 gene on chromosome 16 between SGVP CHS and INS populations explains the workflow involved.
- R script for standardization of genomewide varLD scores
- SGVP CHS-INS standardized varLD scores in chromosome 16 positions 30MB to 32MB (VKORC1 gene) for plotting
- R script for standardized varLD score plot
Please cite the following publication(s) if you are using the program in any publication.
- RTH Ong et al. varLD: A program for quantifying variation in linkage disequilibrium patterns between populations (submitted)
- Teo YY et al.(2009) Genome-wide comparisons of variation in linkage disequilibrium. Genome Research, 19, 1849-1860
If you have any questions regarding the use of the program, please send an e-mail to both of the following people:
- Rick Ong ( firstname.lastname@example.org)
- Dr. Yik Ying Teo ( email@example.com)