picard.addrg: picard.addrg

In omicsCore/SEQprocess: SEQprocess : a modularized and customizable pipeline framework for NGS processing in R package.

Description

A wrapper function to run Picard (AddOrReplaceReadGroups)

Usage

picard.addrg(fns.bam, output.dir, sample.name, RGLB="lC", RGPL="Illumina", RGPU="runbarcode", RGSM, SORT_ORDER="coordinate", VALIDATION_STRINGENCY="LENIENT", CREATE_INDEX=TRUE, tmp.dir=file.path(output.dir, "tmp"), run.cmd=TRUE, mc.cores=1)

Arguments

fns.bam	Path to BAM files
output.dir	Output directory
RGLB	A parameter value for RGLB in picard. A character value of Read Group library (default="LC")
RGPL	A parameter value for RGPL in picard. A character value of Read Group platform (default="Illumina")
RGPU	A parameter value for RGPU in picard. A character value of Read Group platform unit (default="runbarcode")
RGSM	A parameter value for RGSM in picard. character value of Read Group sample name (default=sample.name)
SORT_ORDER	A parameter value for SO in picard. Sort order, a character value of sorting method (default="coordinate")
VALIDATION_STRINGENCY	A parameter value for VALIDATION_STRINGENCY in picard. A character value of validation stringency (default="LENIENT")
CREATE_INDEX	A parameter value for CREATE_INDEX in picard. A character value whether to create .bam index files (default="true")
tmp.dir	Temporary directory path (default=./tmp)
run.cmd	Whether to execute the command line (default=TRUE)
mc.cores	The number of cores to use. Must be at least one(default=1), and parallelization requires at least two cores.
sample.name	A character vector for the sample names

Details

This tool enables the user to replace all read groups in the INPUT file with a single new read group and assign all reads to this read group in the output BAM files.

Value

BAM files added read groups

See Also

http://broadinstitute.github.io/picard/

omicsCore/SEQprocess documentation built on May 7, 2020, 4:18 a.m.