Convert `.bam`-like data to `.vcf` format — bam_to

This function simulates the conversion of `.bam`-like data to `.vcf` format. It creates a dummy `.vcf` file with dummy data.

Usage

bam_to_vcf(
  patient_id,
  output_dir = tempdir(),
  vcf_file = paste0(output_dir, "/", patient_id, ".vcf")
)

Arguments

patient_id: A character string specifying the patient ID. This will be used as the base name for the output `.vcf` file.
output_dir: A character string specifying the directory where the `.vcf` file will be saved.
vcf_file: A character string specifying the path to the output `.vcf` file. Default is "dummy.vcf".

Details

The function creates a dummy `.vcf` file with dummy data. The `.vcf` file contains the following fields: - CHROM: Chromosome name - POS: Position on the chromosome - ID: Variant identifier (dummy value ".") - REF: Reference allele - ALT: Alternate allele - QUAL: Quality score - dg: Total depth - gt: Genotype The function writes the `.vcf` file to the specified path.

Examples

# Convert `.bam`-like data to `.vcf` format
patient_id <- "patient_123"
output_dir <- tempdir()
bam_to_vcf(patient_id, output_dir, vcf_file = paste0(output_dir, "/", patient_id, ".vcf"))
#> Dummy .vcf written to /tmp/RtmpCk48DO/patient_123.vcf