read_table_to_loci.pipeline: Given a read table, split variable positions into loci

In SLeviyang/RegressHaplo: Haplotype Reconstruction Using Penalized Regression

Given a read table, split variable positions into loci

Description

Given a read table, split variable positions into loci

Usage

read_table_to_loci.pipeline(out_dir, max_num_haplotypes = 1200)

Arguments

out_dir	output directory for parameter files and assumed directory of read table
max_num_haplotypes	the maximum number of haplotypes over the full reference that will be considered.

Details

The read table is assumed to be in out_dir with filename read_table.csv. The parameter min_cover can (and should) be used to force loci to break across low coverage regions of the reference.

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