Download HPRC Per-Haplotype CAT Annotations — download_hprc

Downloads the Human Pangenome Reference Consortium year-1 CAT/Liftoff gene annotations of an assembled sample, one GFF3 per haplotype, lifted from GENCODE v38 onto the sample's own assembly in CHM13 or GRCh38 coordinates. The files keep GENCODE identifiers in source_gene / source_transcript, so merge_annotations() and haplotype_summary() can compare haplotypes.

Usage

download_hprc_annotation(
  sample,
  haplotype = c(1L, 2L),
  assembly = c("chm13", "hg38"),
  output_path = ":cache:",
  timeout_limit = 3600,
  method = "auto"
)

Arguments

sample: HPRC sample ID, for example "HG00438" or "HG002".
haplotype: Haplotype numbers to download, 1, 2 or c(1, 2) (default).
assembly: Coordinate space of the CAT run: "chm13" (default) or "hg38".
output_path: Directory where the file is saved. Defaults to ":cache:", the package cache (see get_isoformic_cache()).
timeout_limit: Maximum time in seconds for the download. Takes precedence over options("timeout"). Defaults to 3600.
method: Method used by utils::download.file(). Defaults to "auto".

Value

A named character vector of file paths (names hap1, hap2), ready for merge_annotations().

Examples

if (FALSE) { # \dontrun{
files <- download_hprc_annotation("HG00438")
merged <- merge_annotations(files, annot_name = "HG00438_chm13")
merged
} # }