full_pipeline: Execute full RegressHaplo pipeline

In SLeviyang/RegressHaplo: Haplotype Reconstruction Using Penalized Regression

Execute full RegressHaplo pipeline

Description

Execute full RegressHaplo pipeline

Usage

full_pipeline(
  bam_file,
  out_dir,
  max_num_haplotypes = 800,
  rho_vals = NULL,
  start_pos = NULL,
  end_pos = NULL,
  sig = 0.01,
  num_trials = 700,
  heavy_tail = T
)

Arguments

bam_file	bam file
out_dir	output directory
rho_vals	The values for rho, the penalty parameter, that will be used in the regression. If NULL then RegressHaplo will choose values.
start_pos	Position on the reference at which the reconstruction begins.
end_pos	Position on the reference at which the reconstruction ends
sig	The significance level at which variants should be called.
num_trials	number of trials to run in order to find optimal solution. This number of trials is run for each rho value, unless rho=NULL, in which case this is the total number of trials.
heavy_tail	See comments in help of bam_to_variant_calls.pipeline
max_num_haplotype	The maximum number of haplotype over which the regression will be performed. Lower values mean faster run times but poorer inference. Any number above 1200 will lead to very slow run times.

SLeviyang/RegressHaplo documentation built on June 1, 2022, 10:48 p.m.