Save a data frame as a VCF File — save_as

This function saves a given data frame in variant calling format (VCF) with necessary headers.

Usage

save_as_vcf(data, file, header = NULL)

Arguments

data: A data frame containing variant data (data.frame). The first column should represent the chromosome.
file: A character string specifying the output file path with the .vcf or .vcf.gz extension (character string). If the file has the .vcf.gz extension it will be compressed.
header: An optional custom header for the VCF format (character vector). By default, NULL sets a minimal header.

Value

The function does not return a value but writes a VCF file to the specified path.

Details

The function ensures that the first column is named #CHROM and writes standard VCF headers. It then appends the variant data in a tab-separated format.

Examples

if (FALSE) { # \dontrun{
vcf_data <- data.frame(
  CHROM = c("chr1", "chr2"),
  POS = c(12345, 67890),
  ID = c(".", "."),
  REF = c("A", "T"),
  ALT = c("G", "C"),
  QUAL = c(".", "."),
  FILTER = c("PASS", "PASS"),
  INFO = c("AF=0.5", "AF=0.3"),
  FORMAT = c("GT", "GT"),
  SAMPLE = c("0/1", "1/1")
)
save_as_vcf(vcf_data, "output.vcf")
} # }