Mengci Li, Shouli Wang, Guoxiang Xie, Tianlu Chen and Wei Jia

Genotype Calling with Uncertainty from Sequencing Data in
Polyploids and Diploids
c(person("Lindsay V.", "Clark", email = "lvclark@illinois.edu",
role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-3881-9252")),
person("U.S. National Science Foundation", role = "fnd"))
Lindsay V. Clark [aut, cre] (<https://orcid.org/0000-0002-3881-9252>),
U.S. National Science Foundation [fnd]
rrBLUP, Rsamtools, GenomeInfoDb, Biostrings, GenomicRanges,
VariantAnnotation, SummarizedExperiment, S4Vectors, IRanges,
BiocGenerics, knitr, rmarkdown, GenomicFeatures
Read depth data from genotyping-by-sequencing (GBS) or restriction
site-associated DNA sequencing (RAD-seq) are imported and used to make Bayesian
probability estimates of genotypes in polyploids or diploids.  The genotype
probabilities, or genotypes sampled from those probabilties, can then be exported
for downstream analysis.  'polyRAD' is described by Clark et al. (2018)
<doi:10.1101/380899>.

rrBLUP, Rsamtools, GenomeInfoDb, Biostrings, GenomicRanges,
VariantAnnotation, SummarizedExperiment, S4Vectors, IRanges,
BiocGenerics, knitr, rmarkdown, GenomicFeatures, qqman

Read depth data from genotyping-by-sequencing (GBS) or restriction
site-associated DNA sequencing (RAD-seq) are imported and used to make Bayesian
probability estimates of genotypes in polyploids or diploids.  The genotype
probabilities, or genotypes sampled from those probabilties, can then be exported
for downstream analysis.  'polyRAD' is described by Clark et al. (2019)
<doi:10.1534/g3.118.200913>.

rrBLUP, Rsamtools, GenomeInfoDb, Biostrings, GenomicRanges,
VariantAnnotation, SummarizedExperiment, S4Vectors, IRanges,
BiocGenerics, knitr, rmarkdown, GenomicFeatures, qqman, ggplot2
Read depth data from genotyping-by-sequencing (GBS) or restriction
site-associated DNA sequencing (RAD-seq) are imported and used to make Bayesian
probability estimates of genotypes in polyploids or diploids.  The genotype
probabilities, posterior mean genotypes, or most probable genotypes can then
be exported for downstream analysis.  'polyRAD' is described by Clark et al.
(2019) <doi:10.1534/g3.118.200913>.  A variant calling pipeline for highly
duplicated genomes is also included and is described by Clark et al. (2020)
<doi:10.1101/2020.01.11.902890>.