Filters a vector of variant IDs to those present in the LD reference panel.
Auto-detects the reference type (PLINK2, PLINK1, or pre-computed LD metadata).
Usage
filter_variants_by_ld_reference(
variant_ids,
ld_reference_meta_file,
keep_indel = TRUE
)
Arguments
- variant_ids
variant names in the format chr:pos:ref:alt.
- ld_reference_meta_file
Path to LD metadata file or PLINK prefix.
- keep_indel
Whether to keep indel variants. Default TRUE.
Value
A list with:
- data
Character vector of filtered variant IDs.
- idx
Integer vector of indices into the original variant_ids.