picard.reorder: picard.reorder

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

Description

A wrapper function to run Picard (ReordrSam)

Usage

picard.reorder(fns.bam, output.dir, sample.name, ref.fa, ALLOW_INCOMPLETE_DICT_CONCORDANCE=FALSE, ALLOW_CONTIG_LENGTH_DISCORDANCE=FALSE, CREATE_INDEX=TRUE, run.cmd=TRUE, mc.cores=1)

Arguments

fns.bam	Path to BAM files
output.dir	Output directory
ref.fa	Reference fasta file (eg. GRCh38.fa)
ALLOW_INCOMPLETE_DICT_CONCORDANCE	A parameter value for ALLOW_INCOMPLETE_DICT_CONCORDANCE in picard. Logical, allow discordant contig (default=FALSE)
ALLOW_CONTIG_LENGTH_DISCORDANCE	A parameter value for ALLOW_CONTIG_LENGTH_DISCORDANCE in picard. Logical, allow contig of different length (default=FALSE)
CREATE_INDEX	A parameter value for CREATE_INDEX in picard. Logical, whether to create .bam index files (default=TRUE)
tmp.dir	Temporary directory (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

ReorderSam reorders reads in a BAM file to match the contig ordering in a provided reference file, as determined by exact name matching of contigs. Reads mapped to contigs but absent in the new reference are dropped. Runs substantially faster if the input is an indexed BAM file.

Value

Reordered BAM files (e.g., .rg.od.bam)

See Also

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

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