filter_bam: Filter BAM to specific regions

In TearsWillFall/ULPwgs: An implementation of a wrapper for estimating tumor fraction in ultra-low-pass whole genome sequencing (ULP-WGS) for cell-free DNA in GNU/Unix based systems

Filter BAM to specific regions

Description

This function takes a BAM file and filter it to genomic coordinate or otherwise BED file with multiple genomic coordinates. The output is a BAM file with reads for inputed genomic region/s

Usage

filter_bam(
  bin_samtools = build_default_tool_binary_list()$bin_samtools,
  bam = "",
  position = "",
  bed = "",
  verbose = FALSE,
  batch_config = build_default_preprocess_config(),
  output_dir = ".",
  threads = 1
)

Arguments

bin_samtools	Path to readCounter executable. Default path tools/samtools/samtools.
bam	Path to the BAM file .
position	String of genomic position to filter. Ex chr6:1000-100000
bed	Size of non overlaping windows. Default 500000.
verbose	Enables progress messages. Default False.
output_dir	Path to output directory.
threads	Number of threads to use. Default 1
output_name	Name of the output file.

TearsWillFall/ULPwgs documentation built on April 18, 2024, 3:45 p.m.