Run strelka

Strelka is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs.

Usage

strelka(script, ...)

Arguments

script

Name of the Strelka script. One of "configureStrelkaGermlineWorkflow", "configureStrelkaSomaticWorkflow", and "runWorkflow".

...

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

strelka

A string of path to strelka command.

Value

A command object.

See also

• https://github.com/Illumina/strelka

• 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(), freebayes(), gistic2(), kraken2(), kraken_tools(), minimap2(), perl(), pyscenic(), python(), samtools(), seqkit(), snpEff(), trust4(), varscan()