blit (version 0.2.0)

allele_counter: Run alleleCount

Description

The alleleCount program primarily exists to prevent code duplication between some other projects, specifically AscatNGS and Battenberg.

Usage

allele_counter(
  hts_file,
  loci_file,
  ofile,
  ...,
  odir = getwd(),
  alleleCounter = NULL
)

Value

A command object.

Arguments

hts_file

A string of path to sample HTS file.

loci_file

A string of path to loci file.

ofile

A string of path to the output file.

...

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

odir

A string of path to the output directory.

alleleCounter

A string of path to alleleCounter command.

See Also

• https://github.com/cancerit/alleleCount

• cmd_wd()/cmd_envvar()/cmd_envpath()/cmd_conda()

• cmd_on_start()/cmd_on_exit()

• cmd_on_succeed()/cmd_on_fail()

• cmd_parallel()

Other commands: cellranger(), conda(), fastq_pair(), gistic2(), kraken2(), kraken_tools(), perl(), pyscenic(), python(), samtools(), seqkit(), trust4()