Run bedtools

The bedtools is a powerful toolset for genome arithmetic.

Usage

bedtools(subcmd = NULL, ..., bedtools = NULL)

Arguments

subcmd

Sub-Command of bedtools. Details see: cmd_help(bedtools()).

...

<dynamic dots> Additional arguments passed to bedtools command. Empty arguments are automatically trimmed. If a single argument, such as a file path, contains spaces, it must be quoted, for example using shQuote(). Details see: cmd_help(bedtools()).

bedtools

A string of path to bedtools command.

Value

A command object.

See also

• http://bedtools.readthedocs.io/

• https://github.com/arq5x/bedtools2/

• cmd_wd()/cmd_envvar()/cmd_envpath()/cmd_condaenv()

• cmd_on_start()/cmd_on_exit()

• cmd_on_succeed()/cmd_on_fail()

• cmd_parallel()

Other commands: allele_counter(), bcftools(), bowtie2(), bwa(), cellranger(), conda(), fastp(), fastq_pair(), gistic2(), kraken2(), kraken_tools(), perl(), pyscenic(), python(), samtools(), seqkit(), snpEff(), trust4(), varscan()