assess_vcf_coverage — assess_vcf

Quantifying read depth of all samples in VCF

Usage

assess_vcf_coverage(
  vcf_arrow,
  res_path,
  species,
  project,
  details = TRUE,
  max_points_per_sample = 5000L
)

Arguments

vcf_arrow: -> VCFArrow object
res_path: -> path to results (directory for output dataframe and plots)
species: -> sample name for plot (character)
project: -> project name / base output file name (character)
details: -> flag for adding project name into figure title, default TRUE (Boolean)
max_points_per_sample: -> maximum number of SNVs from which to plot coverage, default 5000 (integer)

Value

violin plot of read depth for each sample in VCF

Details

This function generates a violin plot of read depths per sample.

Author

Tomas Hrbek April 2026

Examples

f <- system.file("extdata", "vaillantii_discosnp_sub.vcf.gz",
                 package = "VCFArrow")
vcf <- read_vcf(f) |> set_vcf_groups(dirname(f))
#> ℹ VCF is being read in chunks of 50000 variants
#> ✔ VCF successfully read into a VCFArrow object
assess_vcf_coverage(vcf, res_path = tempdir(),
                    species = "Phyllomedusa vaillantii",
                    project = "vaillantii")