gatk.targetcreator: gatk.targetcreator

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

Description

A wrapper function to run GATK (RealignerTargetCreator)

Usage

gatk.targetcreator(fns.bam, output.dir, sample.name, ref.fa, ref.indels, unsafe=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
ref.fa	Reference fasta file
ref.gold_indels	Known sites to indel variant call format(VCF)
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

Define insertion and deletion intervals to target for local realignment

Value

Interval file included indel positions (e.g., .intervals)

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.