bwaIndexUcsc: Generating bwa genome index for GATK variant call

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

Generating bwa genome index for GATK variant call

Description

This function executes the docker container bwa1 where BWA is installed. The index is created using GATK bundle data genome fasta file. User needs to dowload the file in the genome folder from ftp://[e-mail]/bundle

Usage

bwaIndexUcsc(
  group = c("sudo", "docker"),
  genome.folder = getwd(),
  uscs.urlgenome = NULL,
  dbsnp.file = NULL,
  g1000.file = NULL,
  gatk = FALSE
)

Arguments

group	a character string. Two options: "sudo" or "docker", depending to which group the user belongs
genome.folder	a character string indicating the folder where the indexed reference genome for bwa will be located
uscs.urlgenome	a character string indicating the URL from uscs download web page for the unmasked genome sequence of interest
dbsnp.file	a character string indicating the name of dbSNP vcf located in the genome folder. The dbSNP vcf, dbsnp_138.b37.vcf.gz and dbsnp_138.hg19.vcf.idx.gz, can be downloaded from ftp://[e-mail]/bundle/b37
g1000.file	a character string indicating the name of 1000 genome vcf located in the genome folder. The 1000 genomes vcf, Mills_and_1000G_gold_standard.indels.b37.vcf.gz and Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.idx.gz, can be downloaded from ftp://[e-mail]/bundle/b37/
gatk	a boolean TRUE and FALSE that indicate if the index will be used for GATK analysis

Value

The indexed bwa genome reference sequence

Author(s)

Raffaele Calogero

Examples

## Not run: 
    #running bwa index
    bwaIndexUcsc(group="sudo",genome.folder="data/genomes/hg19_bwa", uscs.urlgenome=
    "http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz",
    dbsnp.file="dbsnp_138.hg19.vcf.gz", g1000.file="Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz",
    gatk=TRUE)

    #running bwa index
    bwaIndexUcsc(group="sudo",genome.folder="/data/genomes/mm10bwa", uscs.urlgenome=
    "http://hgdownload.cse.ucsc.edu/goldenPath/mm10/bigZips/chromFa.tar.gz",
    gatk=FALSE)



## End(Not run)

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