full_pipeline | R Documentation |
Execute full RegressHaplo pipeline
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 )
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. |
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