gatk: Calls the GATK executable

In HenrikBengtsson/aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

Description

Calls the GATK executable.

Usage

 ## Default S3 method:
gatk(analysisType, ..., pathnameI=NULL, pathnameR=NULL, pathnameL=NULL, pathnameLog=NULL,
  outPath=NULL, overwrite=FALSE, verbose=FALSE)

Arguments

analysisType	(required) A character string specifying type of analysis. In GATK, this corresponds to engine argument --analysis_type (or -T).
...	(optional) named arguments

.

pathnameI	(optional) A character vector specifying one or more (SAM or BAM) files. In GATK, this corresponds to one or more engine arguments --input_file (or -I).
pathnameR	(optional) A character string specifying a reference file. In GATK, this corresponds to engine argument --reference_sequence (or -R).
pathnameL	(optional) A character string specifying a ROD file. In GATK, this corresponds to engine argument --interval (or -L).
outPath	Directory where result files are written.
verbose	See Verbose.

Author(s)

Henrik Bengtsson

References

[1] GATK: The Genome Analysis Toolkit, Broad Institute, 2014. http://www.broadinstitute.org/gatk/

HenrikBengtsson/aroma.seq documentation built on Feb. 15, 2021, 2:21 a.m.