kohlkopf / GUS-LD

Genotyping Uncertainty with Sequencing data - Linkage Disequilibrium

GUS-LD Version 0.1.1

Genotyping Uncertainty with Sequencing data - Linkage Disequilibrium (GUS-LD).

R code that implements the method introduced by Bilton et al. (2018) that estimates linkage disequilibrium using low coverage sequencing data that have been generated using high-throughput sequencing multiplexing methods, such as genotyping-by-sequencing, restriction-site association DNA or exome-capture. The novelty of this methodology is its ability to account for genotyping errors resulting from low read depths (e.g., allelic dropout).

Data Format:

The key data to use this package are:

• genon: Matrix of genotype calls, which are coded 2 = homozygous genotype for the reference allele, 1 = heterozygous genotype, 0 = homozygous genotype for the alternate allele. The rows must correspond to the number of individuals and columns correspond to the number of SNPs.
• depth_Ref: Matrix of allele counts for the reference allele associated with each genotype call. This matrix corresponds to the matrix of genotype calls (e.g., the i^th row and j^th column in depth is the read depth corresponding to the i^th row and j^th column in the genon matrix).
• depth_Alt: Matrix of allele counts for the alternate allele associated with each genotype call. This matrix corresponds to the matrix of genotype calls (e.g., the i^th row and j^th column in depth is the read depth corresponding to the i^th row and j^th column in the genon matrix).

To convert data from VCF format into the required format, use the function 'readVCF' which is available in the script readVCF.R. For example,

source("readVCF.R")
data <- readVCF("vcffilename.vcf")

Files:

• GUS-LD.R: R script which contains a function for computing all the pairwise LD estimates in the data. Note that parallelization is possible in this function but requires that the foreach and doSNOW R packages are installed.
• GUS-LD-example.R: R script with some example code using the deer dataset found in Bilton et al. (2018).
• deer.RData: Matrix of genotype calls and allele counts for reference and alternate alleles for the deer dataset used in Bilton et al. (2017).
• readVCF.R: R script with functions for converting a VCF file into the required format for GUS-LD.

Example:

The best way to understand how GUS_LD works is to run through the file GUS_LD-example.R.

References:

Bilton, T.P., McEwan, J.C., Clarke, S.M., Brauning, R., Van Stijn, T.C., Rowe, S.J., Dodds, K.G. (2018). Linkage disequilibrium estimation in low coverage high-throughput sequencing data. Genetics, 209(2), 289-400. doi:10.1534/genetics.118.300831

License

GUS-LD is Copyright (C) 2017-2018 AgResearch Ltd., released under the GNU General Public License version 3.