picard.collectmetrics: picard.collectmetrics

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

Description

Provide read alignment information.

Usage

picard.collectmetrics(fns.bam, out.fns, ref.fa, run.cmd=T, mc.cores=1)

Arguments

fns.bam	Path to BAM files
ref.fa	Reference fasta file path
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.
output.dir	Output directory

Details

Provides a summary of the alignment process using the bam files

Value

txt files

Author(s)

Ji-Hye Lee

References

Currently there is no journal reference for picard.

See Also

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

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