alignment_bwa: Read alignment using BWA

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

Read alignment using BWA

Description

This function aligns a sequence of reads to a reference genome using a Burrows-Wheeler aligner. The reference genome has to be previously been sorted and indexed. It generates a BAM file with the aligned sequence.

Usage

alignment_bwa(
  bin_bwa = build_default_binary_list()$alignment$bin_bwa,
  bin_samtools = build_default_binary_list()$alignment$bin_samtools,
  file_R1 = "",
  file_R2 = "",
  threads = 3,
  ram = 4,
  id_tag = "NA",
  pu_tag = "NA",
  pl_tag = "ILLUMINA",
  lb_tag = "NA",
  sm_tag = "",
  sort = TRUE,
  coord_sort = TRUE,
  index = TRUE,
  clean = TRUE,
  stats = "all",
  ref_genome = "",
  output_dir = ".",
  verbose = FALSE,
  batch_config = build_default_preprocess_config(),
  executor_id = make_unique_id("alignment"),
  task_name = "alignment",
  mode = "local",
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

bin_bwa	Path to bwa executable. Default path tools/bwa/bwa.
bin_samtools	Path to samtools executable. Default path tools/samtools/samtools.
file_R1	Path to the input file with the sequence.
file_R2	Optional Path to the input with the reverse read sequence.
threads	Number of CPU cores to use. Default 3.
ram	RAM memory to use for sorting and indexing. Provided in GB.
id_tag	Read group identifier. Default NA.
pu_tag	Platform unit identifier. Default NA.
pl_tag	Platform/technology used to produce the read. Default "ILLUMINA". Options "ILLUMINA","SOLID", "LS454", "HELICOS","PACBIO"
lb_tag	DNA preparation library identifier.
sm_tag	Sample name tag. If not given will use sample name as default.
sort	Sort aligned file. Default TRUE.
coord_sort	Sort BAM file by coordinate. Alternatively sort by name. Default TRUE.
index	Generate index file if BAM sorted by coordinate. Default TRUE.
clean	Clean intermediary files. Default TRUE.
stats	Generate BAM stats. Default all. Options "all","flag","index",""
ref_genome	Path to input file with the reference genome sequence.
output_dir	Path to the output directory.
verbose	Enables progress messages. Default False.
executor_id	Task EXECUTOR ID. Default "alignment"
mode	REQUIRED Where to parallelize. Default local. Options "local","batch"
time	OPTIONAL If batch mode. Max run time per job. Default "48:0:0"
update_time	OPTIONAL If batch mode. Job update time in seconds. Default 60.
wait	OPTIONAL If batch mode wait for batch to finish. Default FALSE
task_nam	Task nam. Default "alignment"

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