write_vcf {jackalope}

Write haplotype info from a haplotypes object to a VCF file.

Description

Compression in this function always uses "bgzip" for compatibility with "tabix".

Usage

write_vcf(
  haps,
  out_prefix,
  compress = FALSE,
  sample_matrix = NULL,
  show_progress = FALSE,
  overwrite = FALSE
)

Arguments

haps

A haplotypes object.

out_prefix

Prefix for the output file.

compress

Logical specifying whether or not to compress output file, or an integer specifying the level of compression, from 1 to 9. If TRUE, a compression level of 6 is used. Defaults to FALSE.

sample_matrix

Matrix to specify how haplotypes are grouped into samples if samples are not haploid. There should be one row for each sample, and each row should contain indices or names for the haplotypes present in that sample. Indices/names for haplotypes cannot be repeated. Instead of repeating indices here, you should use the dup_haps method of the haplotypes class to duplicate the necessary haplotype(s). The number of columns indicates the ploidy level: 2 columns for diploid, 3 for triploid, 4 for tetraploid, and so on; there is no limit to the ploidy level. If this argument is NULL, it's assumed that each haplotype is its own separate sample. Defaults to NULL.

show_progress

Logical for whether to show a progress bar. Defaults to FALSE.

overwrite

Logical for whether to overwrite existing file(s) of the same name, if they exist. Defaults to FALSE.

Value

NULL