This is the GitHub repository for the manuscript "SNP genotyping and parameter estimation in polyploids using low-coverage sequencing data," which is currently under peer review. We have also posted a preprint on bioRxiv.
ebg/: C++ source code for EM/ECM algorithms for genotyping with our models.
helper-scripts/: Python, Perl, R, and Bash scripts for extracting and filtering allele depth info from a VCF file for use with
Rcode/: R and C++ code for performing simulations and for running analyses.
data/: example data sets from Betula pendula, B. pubescens, and Andropogon gerardii that were used in the manuscript.
docs/: Rmd and HTML files for GitHub pages site.
More details on the contents of each folder can be found in their respective README files.