VarScan is a platform-independent software tool developed at the Genome Institute at Washington University to detect variants in NGS data.

VarScan is a platform-independent software tool developed at the Genome Institute at Washington University to detect variants in NGS data.

Usage

varscan(subcmd = NULL, ..., varscan = NULL)

Arguments

subcmd

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

...

<dynamic dots> Additional arguments passed to varscan 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(varscan()).

varscan

A string of path to varscan command.

Value

A command object.

See also

• https://varscan.sourceforge.net/

• 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(), bedtools(), bowtie2(), bwa(), cellranger(), conda(), fastp(), fastq_pair(), gistic2(), kraken2(), kraken_tools(), perl(), pyscenic(), python(), samtools(), seqkit(), snpEff(), trust4()