variant_calls_to_read_table.pipeline: Given variant calls and a bam file, create a read table

In SLeviyang/RegressHaplo: Haplotype Reconstruction Using Penalized Regression

Given variant calls and a bam file, create a read table

Description

Given variant calls and a bam file, create a read table

Usage

variant_calls_to_read_table.pipeline(
  bam_file,
  out_dir,
  use_raw_read_table = F,
  sig = 0.01,
  debug = F
)

Arguments

bam_file	path to bam file
out_dir	output directory, will be created if needed
use_raw_read_table	If there is an existing raw_read_table.csv file, should it be used as a raw read table? See details.
sig	significance levels at which to filter reads.

Details

Converts bam_file to a raw read table, written to $outdir/raw_read_table.csv and then applies error correction to reads and creates a filtered read table, written to $outdir/read_table.csv. The parameter use_raw_read_table can be used to skip the step of creating the raw read table, which is very time consuming. This is particularly useful, if the user wants to experiment with different error levels to form an acceptable read table.

Value

path to read table file

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