Genetic variant annotation, and functional effect prediction toolbox. It annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes).

Genetic variant annotation, and functional effect prediction toolbox. It annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes).

Usage

snpEff(subcmd = NULL, ..., snpEff = NULL)

Arguments

subcmd

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

...

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

snpEff

A string of path to snpEff command.

Value

A command object.

See also

• https://pcingola.github.io/SnpEff/

• 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(), trust4(), varscan()