picard.rmdu: picard.rmdu

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

Description

A wrapper function to run Picard (MarkDuplicates)

Usage

picard.rmdu(fns.bam, output.dir, sample.name, out.metrics, CREATE_INDEX=TRUE, REMOVE_DUPLICATES=TRUE, VALIDATION_STRINGENCY="LENIENT", tmp.dir=file.path(output.dir, "tmp"), BARCODE_TAG=FALSE, run.cmd=TRUE, mc.cores=1)

Arguments

fns.bam	Path to BAM files
output.dir	Output directory
sample.name	A character vector for the sample names
CREATE_INDEX	A parameter value for CREATE_INDEX in picard. Logical, whether to create bam index files (default=TRUE)
REMOVE_DUPLICATES	A parameter value for REMOVE_DUPLICATES in picard. Logical, whether to remove duplicates (default=TRUE)
VALIDATION_STRINGENCY	A parameter value for VALIDATION_STRINGENCY in picard. A character value of validation stringency (default="LENIENT")
tmp.dir	Temporary directory (default= ./tmp)
BARCODE_TAG	A parameter value for BARCODE_TAG in picard. If barcode sequencing data, set this option TRUE. Duplicated BARCODE is removed.
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.#' @details The MarkDuplicates tool works by comparing sequences in the 5 prime positions of both reads and read-pairs in a SAM/BAM file. An BARCODE_TAG option is available to facilitate duplicate marking using molecular barcodes. After duplicate reads are collected, the tool differentiates the primary and duplicate reads using an algorithm that ranks reads by the sums of their base-quality scores.

Value

Removing duplicate reads in bam files (e.g., .rmdu.bam)

See Also

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

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