Build a reference panel using population-specific filters

Usage

niptmer_ref_build(
  base_panel_dir = NULL,
  reference_fasta_dir = NULL,
  genome_fasta = NULL,
  pop_vcf_files = NULL,
  pop_bed_files = NULL,
  control_lists = NULL,
  control_fastq = NULL,
  k = 25,
  strategy = c("paper_plus_population", "from_scratch"),
  out_dir = ".",
  chr_ids = c(as.character(seq_len(22L)), "X", "Y"),
  min_af = 0.01,
  vcf_engine = c("legacy_compatible", "simple"),
  profile = NULL,
  pool_mode = c("block", "none"),
  model = c("poisson", "nbinom"),
  distribution_max = 500,
  lower_p = 0.01,
  upper_p = 0.99,
  block_size = 50,
  min_block_support = 0.7
)

Arguments

base_panel_dir: Directory with initial per-chromosome list files. Required for strategy = "paper_plus_population".
reference_fasta_dir: Directory of per-chromosome FASTA files used for VCF blacklist generation and for strategy = "from_scratch" list generation.
genome_fasta: Genome FASTA for BED blacklist generation.
pop_vcf_files: Optional population VCF files.
pop_bed_files: Optional population BED files.
control_lists: Optional control list files for stability whitelist.
control_fastq: Optional control FASTQ/FASTA files.
k: K-mer size.
strategy: Build strategy.
out_dir: Output directory.
chr_ids: Chromosomes to include.
min_af: Minimum AF for VCF blacklist.
vcf_engine: Variant expansion mode used by niptmer_ref_blacklist_from_vcf().
profile: Optional named list of default tuning parameters. Use niptmer_ref_profile_ulcwgs() for recommended ULCWGS settings.
pool_mode: Pooling mode passed to niptmer_ref_stability_whitelist().
model: Count model passed to niptmer_ref_stability_whitelist().
distribution_max: Max distribution count for NB estimation.
lower_p: Lower Poisson cutoff.
upper_p: Upper Poisson cutoff.
block_size: Controls per block for whitelist building.
min_block_support: Block support threshold for stable whitelist.

Value

A niptmer_ref_panel object after applied filters.