vcf2gt_long

Converts a VCFArrow object to tidy long format infile

Usage

vcf2gt_long(
  vcf_arrow,
  out_file,
  keep_groups = NULL,
  format = c("feather", "parquet", "csv"),
  col_select = NULL
)

Arguments

vcf_arrow

-> VCFArrow object

out_file

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

keep_groups

-> groups to retain, default NULL (character)

format

-> one of three output formats (arrow, parquet, CSV) (character)

col_select

-> optional selection of columns to save, default ALL

Value

Invisibly returns the path of the written file.

Details

This function converts a VCFArrow object to an external SmartSNP 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. The tidy data can be saved in either Arrow, Parquet or CSV formats. File extension is added automatically if missing. Optionally, specific columns can be saved, by default all columns are saved. The gt long slot contains pre-calculated metrics in addition to just genotypes.

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
vcf2gt_long(vcf, out_file = tempfile(), format = "csv")
#> ℹ Writing gt_long: 9313 variants x 18 samples
#> ✔ gt_long table written to /tmp/RtmpSpcr9J/file1ff836277e92.csv