write_vcf

Write a VCFArrow object to an external VCF file

Usage

write_vcf(vcf_arrow, out_file, gzip = FALSE)

Arguments

vcf_arrow

-> VCFArrow object

out_file

-> name of the VCF file to be written to, no default (character)

gzip

-> a flag to GZIP VCF when writing, default FALSE (Boolean)

Value

Invisibly returns the path of the written file.

Details

This function writes a VCFArrow object to an external VCF file. Writing occurs in chunks whose size is determined by the read_vcf() function. Larger chunks result in faster writing speeds. It writes both uncompressed and gz compressed files. Compressing increases writing time be about 50%. For large files, it is recommended to output an uncompressed VCF file, and then compress with GZIP or PIGZ.

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
write_vcf(vcf, out_file = tempfile(fileext = ".vcf"))
#> ℹ VCF is being written in 1 chunk
#> ✔ VCFArrow object successfully written to /tmp/RtmpSpcr9J/file1ff8566e3eb1.vcf
write_vcf(vcf, out_file = tempfile(fileext = ".vcf.gz"),
          gzip = TRUE)
#> ℹ VCF is being written in 1 chunk
#> ✔ VCFArrow object successfully written to /tmp/RtmpSpcr9J/file1ff8142c7d04.vcf.gz