full_pipeline: Execute full RegressHaplo pipeline

full_pipelineR Documentation

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.