write_vcf {jackalope} | R Documentation |
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 |
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 |
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 |
show_progress |
Logical for whether to show a progress bar.
Defaults to |
overwrite |
Logical for whether to overwrite existing file(s) of the
same name, if they exist. Defaults to |
Value
NULL