Uses bundled bcftools to count variants efficiently. For indexed files,
this is very fast. Can also count per-chromosome.
Usage
vcf_count_variants(filename, region = NULL)
Arguments
- filename
Path to VCF/BCF file
- region
Optional region string (e.g., "chr1" or "chr1:1-1000")
Value
Integer count of variants
Examples
if (FALSE) { # \dontrun{
# Total variants
n <- vcf_count_variants("variants.vcf.gz")
# Variants on chr1
n_chr1 <- vcf_count_variants("variants.vcf.gz", region = "chr1")
} # }