Build a population stability whitelist from euploid controls — niptmer_ref_stability

For ultra-low-coverage cohorts, use pool_mode = "block" so filtering is applied to pooled control blocks instead of individual samples.

Usage

niptmer_ref_stability_whitelist(
  control_lists = NULL,
  control_fastq = NULL,
  k = 25,
  pool_mode = c("block", "none"),
  block_size = 50,
  n_blocks = NULL,
  depth_mode = c("auto", "given"),
  depth_values = NULL,
  model = c("poisson", "nbinom"),
  distribution_max = 500,
  lower_p = 0.01,
  upper_p = 0.99,
  min_block_support = 0.7,
  out_prefix = "stable_whitelist",
  out_dir = ".",
  threads = 1
)

Arguments

control_lists: Optional vector of pre-built GenomeTester4 list files.
control_fastq: Optional vector of FASTQ/FASTA files. If provided, per-sample lists are built with glistmaker.
k: K-mer size.
pool_mode: Either "block" or "none".
block_size: Number of controls per block when pool_mode = "block".
n_blocks: Optional explicit number of blocks.
depth_mode: Either "auto" (estimate from each pooled list) or "given" (use depth_values).
depth_values: Optional numeric depth values for each block when depth_mode = "given".
model: Distribution model used for cutoff estimation: "poisson" or "nbinom".
distribution_max: Maximum count inspected from glistquery --distribution when estimating coverage/dispersion.
lower_p: Lower cumulative probability cutoff.
upper_p: Upper cumulative probability cutoff.
min_block_support: Minimum support threshold across blocks. If <= 1, interpreted as a fraction; otherwise interpreted as number of blocks.
out_prefix: Output prefix for final whitelist.
out_dir: Output directory.
threads: Number of threads used when building lists from FASTQ.

Value

A list with final whitelist path and block-level diagnostics.