bwaAlignment: bwaAlignment

In msubirana/ergWgsTools: What the Package Does (One Line, Title Case)

Description

Aligns FASTQ files using bwa mem and a defined reference genome. It alignes fastq paired or single end data. The BAM to FASTQ conversion can be carried out using bamTofastqPicard function.

Usage

bwaAlignment(
  fastq,
  ref,
  out_path,
  threads,
  sambamba = "sambamba",
  bwa = "bwa",
  samblaster = "samblaster",
  samtools = "samtools"
)

Arguments

fastq	Fastq file to carry the analysis. If paried-end type, 'input_file' have to contain mate 1s and different pairs should be named "_R1" or "_R2". Allowed formats: fastq.gz, fq.gz, fastq, fq or bam.
ref	Path for the reference genome to use for the alignment (fasta format) and the corresponding indexes generated with bwa index and a dictionary index file generated by CreateSequenceDictionary gatk tool.
out_path	Path where the output of the analysis will be saved.
threads	Number of threads to use in the analysis.
sambamba	Path of sambamba binary
bwa	Path of bwa binary.
samblaster	Path of samblaster binary.
samtools	Path of samtools binary.

Examples

## Not run: 
bwaAlignment(fastq = 'raw/sample_R1.fa',
             ref = 'ref/hg38.fa',
             out_path = 'rst',
             threads = 2)

## End(Not run)

msubirana/ergWgsTools documentation built on June 8, 2020, 8:07 a.m.