run_ustacks_one_sample: run_ustacks_one_sample

In thierrygosselin/stackr: Run stacks software pipeline for RADseq analysis inside R

Description

run ustacks for 1 sample

Usage

run_ustacks_one_sample(
  mismatch.testing = FALSE,
  sample.list = NULL,
  project.info = NULL,
  f = "04_process_radtags",
  o = "06_ustacks_2_gstacks",
  m = 3,
  M = 2,
  N = M + 2,
  t = "guess",
  R = FALSE,
  H = TRUE,
  parallel.core = parallel::detectCores() - 1,
  h = FALSE,
  d = TRUE,
  keep.high.cov = FALSE,
  high.cov.thres = 3,
  max.locus.stacks = 3,
  k.len = NULL,
  max.gaps = 2,
  min.aln.len = 0.8,
  disable.gapped = FALSE,
  model.type = "snp",
  alpha = 0.05,
  bound.low = 0,
  bound.high = 0.2,
  bc.err.freq = NULL
)

thierrygosselin/stackr documentation built on Nov. 11, 2020, 11 a.m.