Write mutation_data to a VCF file — write_vcf_from

Export your mutation_data to a VCF file for downstream applications.

Usage

write_vcf_from_mut(mutation_data, output_path = NULL)

Arguments

mutation_data: A data frame of a GRanges object containing your mutation data. This can be the output of import_mut_data, import_vcf_data, or filter_mut. Coordinates must be 1-based. Required columns are "contig", "start", "end", "ref", "alt", "sample", "alt_depth", "total_depth", and "ref_depth". Additional columns are allowed.
output_path: The directory where the VCF file should be written. Default is NULL, which will write the file to the current working directory.

Value

Writes a VCF file of mutations "mutation_output.vcf".

Examples

if (FALSE) { # \dontrun{
example_file <- system.file("extdata", "Example_files",
                            "example_mutation_data_filtered.rds",
                            package = "MutSeqR")
example_data <- readRDS(example_file)
write_vcf_from_mut(example_data)
} # }