Build a pedigree from SNP genotypes with tunable thresholds

Usage

build_pedigree(
  geno,
  s_threshold = 0.65,
  me_max = 0.005,
  oh_max = Inf,
  use_sex = TRUE,
  use_age = FALSE,
  min_parent_gap = 1,
  top_k = Inf,
  preset = c("none", "high_precision", "high_coverage"),
  verbose = TRUE
)

Arguments

geno: List from read_genotypes() containing G, ids, map, meta.
s_threshold: Minimum pairwise similarity for candidate parent-offspring.
me_max: Maximum Mendelian error rate to accept a trio.
oh_max: Maximum opposing homozygotes per candidate.
use_sex: If TRUE, restrict sires to Sex == "M" and dams to Sex == "F".
use_age: If TRUE, require parents be older than offspring.
min_parent_gap: Minimum years older than offspring.
top_k: Keep top-k candidates per offspring per role before trio check.
preset: One of "none", "high_precision", "high_coverage".
verbose: Print progress.

Value

A list with pedigree, assignments, trios, summary, and settings.