Prepare and Index a VCF Input

Accepts plain VCF and compressed VCF input. Existing indexed BGZF files are reused. Missing indexes are created when possible. Plain VCF, ordinary gzip, read-only compressed input, and files that cannot be indexed directly are sorted and converted to an indexed BGZF copy using bcftools.

Usage

prepare_vcf_input(vcf, cache_dir, force = FALSE)

Arguments

vcf

Path to a .vcf or .vcf.gz file.

cache_dir

Directory used for normalized cached inputs.

force

Recreate the normalized cached copy and index.

Value

A list containing path, index, source, and normalized.