Liftover a VCF of variants with CrossMap (allele-aware)

Thin, experimental wrapper around CrossMap vcf, which performs allele-aware variant liftover (updating the REF allele against the target genome and handling strand flips) – something plain interval liftover does not do. Requires CrossMap on the PATH and a target-genome FASTA.

Usage

liftover_vcf(
  vcf,
  chain,
  ref_fasta,
  out = tempfile(fileext = ".vcf"),
  from = NA_character_,
  to = NA_character_,
  crossmap = NULL
)

Arguments

vcf

Path to the input VCF.

chain

Path to a chain file.

ref_fasta

Path to the target-genome FASTA.

out

Output VCF path. Defaults to a temporary file.

from, to

Optional provenance strings.

crossmap

Path or name of the CrossMap executable. Defaults to auto-detection on the PATH.

Value

A TranslationResult whose mapped and unmapped carry the output and unmapped VCF paths; stats records the number of unmapped records.

Details

This function is experimental and intentionally minimal: it runs CrossMap and reports the produced paths and unmapped count rather than parsing variants into R. Parse the output VCF with your tool of choice (e.g. VariantAnnotation).

See also

liftover_intervals(), liftover_crossmap()

Examples

if (FALSE) { # \dontrun{
# Not run: needs CrossMap on the PATH, a chain file, and the target
# genome as a FASTA file, none of which ship with the package.
res <- liftover_vcf(
  vcf = "calls.rn7.vcf",
  chain = "rn7ToHg38.over.chain",
  ref_fasta = "hg38.fa",
  from = "rn7",
  to = "hg38"
)
res@mapped$path # the lifted VCF
res@unmapped$path # the records CrossMap could not place
res@stats$n_unmapped
} # }