bamTofastqPicard: bamTofastqPicard

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

Description

This function converts BAM files to FASTQ files using GATK4 SamToFastq. Type of BAM file (paried or single) is detected automatically.

Usage

bamTofastqPicard(
  bam,
  ref,
  out_path,
  threads,
  gatk4 = "/imppc/labs/lplab/share/bin/gatk-4.1.3.0/gatk",
  sambamba = "sambamba",
  samtools = "samtools"
)

Arguments

bam	Bam file to carry the analysis.
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.
gatk4	Path of GATK4 binary.
sambamba	Path of sambamba binary
samtools	Path of samtools binary.

Examples

## Not run: 
bamTofastqPicard(bam = 'raw/sample.bam',
             ref = 'ref/hg38.fa',
             out_path = 'rst',
             threads = '2')

## End(Not run)

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