Uses bcftools index –stats to get per-contig variant counts.
Requires an indexed file.
Usage
vcf_count_per_contig(filename)
Arguments
- filename
Path to VCF/BCF file (must be indexed)
Value
Named integer vector (names = contigs, values = variant counts)
Examples
if (FALSE) { # \dontrun{
counts <- vcf_count_per_contig("variants.vcf.gz")
# chr1: 12345, chr2: 23456, ...
} # }