get_sq_bam: Function to extract SQ (Reference sequence dictionary)

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

Function to extract SQ (Reference sequence dictionary)

Description

This function takes a BAM file and collects the chr names from the bam file.

Usage

get_sq_bam(
  bin_samtools = build_default_tool_binary_list()$bin_samtools,
  bin_bgzip = build_default_tool_binary_list()$bin_bgzip,
  bin_tabix = build_default_tool_binary_list()$bin_tabix,
  bam = NULL,
  header = TRUE,
  chromosomes = NULL,
  base = 0,
  index = FALSE,
  compress = FALSE,
  ...
)

Arguments

bin_samtools	Path to samtools executable. Default path tools/samtools/samtools.
bam	Path to directory with BAM files to merge.
header	Save header in BED file.

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