gbs: Genotype calls for GBS

In jendelman/polyBreedR: Genomics-assisted breeding for polyploids (and diploids)

Genotype calls for GBS

Description

Genotype calls for genotype-by-sequencing (GBS) data

Usage

gbs(
  in.file,
  out.file,
  ploidy,
  bias = TRUE,
  n.core = 1,
  chunk.size = 1000,
  silent = FALSE,
  model.fit = TRUE
)

Arguments

in.file	VCF input file
out.file	VCF output file
ploidy	ploidy
bias	TRUE/FALSE, whether to estimate allelic bias
n.core	number of cores
chunk.size	number of variants to process at a time
silent	TRUE/FALSE
model.fit	TRUE/FALSE

Details

VCF input file must contain AD field. Variants with more than 2 alleles are coerced to zero DP, so better to filter them out first.

Posterior mode and mean genotypes are added as GT and DS fields. GQ is also added based on probability of posterior mode. Binomial calculation uses R/updog package (Gerard et al. 2018) with "norm" prior. Previous INFO is discarded; adds NS, DP.AVG, AF.GT, AB, OD, SE.

When model.fit is FALSE, the software uses AB, OD, and SE parameters from INFO.

The input file is processed in chunks of size chunk.size.

Value

nothing

jendelman/polyBreedR documentation built on Jan. 5, 2025, 12:13 a.m.