gatk.printreads: gatk.printreads

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

Description

A wrapper function to run GATK (PrintReads)

Usage

gatk.printreads(fn.realign.bam, output.dir, sample.name, ref.fa, fns.grp, unsafe=FALSE, run.cmd=TRUE, mc.cores=1)

Arguments

fns.bam	Path to input BAM files
fns.grp	GATK report file created by BaseRecalibrator
output.dir	Output directory
sample.name	A character vector for the sample names
ref.fa	Reference fasta file
unsafe	A parameter value for -U ALLOW_N_CIGAR_READS in GATK. This parameter must be TRUE in RNA-seq data.
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

Writes a new file using reads from SAM format file (SAM/BAM/CRAM) that pass criteria. Improves the accuracy of variant calling based on Base Quality Score Recalibration.

Value

GATK PrintReads returns a Base quality score recalibrated BAM files (eg. recal.bam)

References

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

See Also

https://software.broadinstitute.org/gatk/

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