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

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

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

Raffaele Calogero

Examples

if (FALSE) {
    #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")

}