vcf2fineradstructure

Converts a VCFArrow object to FineRadStructure format infile

Usage

vcf2fineradstructure(vcf_arrow, out_file, keep_groups = NULL)

Arguments

vcf_arrow

-> VCFArrow object

out_file

-> name of file to output, no default (character)

keep_groups

-> groups to retain, default NULL (character)

Value

Invisibly returns the input VCFArrow object; called for its side effect of writing out_file.

Details

This function converts a VCFArrow object to an external Treemix formatted file. Writing occurs in chunks whose size is determined by the read_vcf() function. Larger chunks result in faster writing speeds. If no groups are defined, the default behavior is to use all groups.

Author

Tomas Hrbek May 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_linked <- vcf_filter_multiSNV(vcf)
#> ℹ Applying linked SNV filter
#> ℹ Retained 8 / 10000 variants (linked SNVs)
vcf2fineradstructure(vcf_linked, out_file = tempfile(fileext = ".txt"))
#> ℹ Building fineRADstructure: 8 variants x 18 samples (0 MiB raw storage)
#> ℹ Writing fineRADstructure file...
#> ✔ fineRADstructure file written to /tmp/RtmpSpcr9J/file1ff8769fbf34.txt