wgsSomaticPreprocessing: wgsSomaticPreprocessing

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

Description

Align, infer the coverage and the quality of the bam or fastq files

Usage

wgsSomaticPreprocessing(
  inputFile,
  ref,
  outPathBam,
  threads,
  removeOpt = "no",
  rstPath
)

Arguments

inputFile	Fastq or bam file to analyse
ref	Reference genome
outPathBam	Path where to save the output bam
threads	Number of threads to use in the analysis
removeOpt	Remove the old bam in the case of the bam realignment
rstPath	Path where to save the coverage and quality results. A 'coverage' and 'fastqc' folders will be created.

Examples

## Not run: 

inputFile <- '/imppc/labs/lplab/share/marc/insulinomas/raw/fastq/NET-25_BL_R1.fq.gz'
ref <- '/imppc/labs/lplab/share/marc/refgen/hg38/hg38.fa'
outPathBam <- '/imppc/labs/lplab/share/marc/insulinomas/processed/hg38/bam/bwa'
threads <- 4
removeOpt <- 'no'
rstPath <- '/imppc/labs/lplab/share/marc/insulinomas/rst'
wgsSomaticPreprocessing(inputFile = inputFile,
                        ref = ref,
                        outPathBam = outPathBam,
                        threads = threads,
                        removeOpt = removeOpt,
                        rstPath = rstPath)

## End(Not run)

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