vcf_stats — vcf_stats • VCFArrow

Calculates basic stats of each samples from VCFArrow format data. Includes average read depth per individual, missing data per individual, Watterson's theta and pi.

Usage

vcf_stats(vcf_arrow, res_path, project, theta = FALSE)

Arguments

vcf_arrow: -> VCFArrow object
res_path: -> directory where to write results
project: -> base name of the project file
theta: -> flag to perform theta and pi calculation, default FALSE (Boolean)

Value

table of statistics

Details

This function calculates average read depth, heterozygosity number of heterozygotes, number of reference and alternative homozygotes, missing data and total number SNPs of each sample in an VCFArrow object. Optionally calls vcf_theta() to get total and group Watterson's theta and pi.

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
vcf_stats(vcf, res_path = tempdir(), project = "vaillantii",
          theta = TRUE)
#> ℹ Computing per-sample stats: 10000 variants x 18 samples, reading 1 chunk directly