snvPreprocessing: Running indel relignment and quality recalibration on bam...

In kendomaniac/docker4seq: Running NGS computing demanding applications, e.g reads mapping and counting, wrapped in docker containers

Running indel relignment and quality recalibration on bam generated by bwa function NOT READY TO GO ON STABLE

Description

This function executes the docker container snvPreprocessing. IMPORTANT: the working folder require the presence of GenomeAnalysisTK.tar.bz2 files

Usage

snvPreprocessing(
  group = c("sudo", "docker"),
  bam.folder = getwd(),
  scratch.folder = "/data/scratch",
  genome.folder,
  threads = 8,
  gatk.file
)

Arguments

group	a character string. Two options: "sudo" or "docker", depending to which group the user belongs
bam.folder	a character string indicating where bam file generated by bwa is located
scratch.folder	a character string indicating the scratch folder where docker container will be mounted
genome.folder	a character string indicating the folder where the index reference genome for bwa is located
threads	a number indicating the number of cores to be used by the application
gatk.file	a character string for GenomeAnalysisTK-X.Y.tar.bz2, this file should be located in the bam.folder

Value

bam and bai after indel relignment and quality recalibration.

Author(s)

Raffaele Calogero

Examples

## Not run: 
    #downloading examples 1 million reads of mcf7 exome mixed with 1 million of mouse derived by human exome capturing
    system("wget http://130.192.119.59/public/hs1m_mm1m_R1.fastq.gz")
    system("wget http://130.192.119.59/public/hs1m_mm1m_R2.fastq.gz")
    
    #required for bwa 61Gb At the present time this is required to run mutect1
    system("wget http://130.192.119.59/public/hg19_exome.tar.gz")
    #this genome index is prepared to be used for indel realignment and quality recalibration
    
    #running snvPreprocessing
    snvPreprocessing(group="docker",bam.folder=getwd(), 
               scratch.folder="/data/scratch",
               genome.folder="/data/scratch/hg19_exome", 
               threads=24, gatk.file="GenomeAnalysisTK-3.7.tar.bz2")


## End(Not run)

kendomaniac/docker4seq documentation built on Sept. 3, 2024, 6:42 p.m.