allele_counter: Run alleleCount

In blit: Bioinformatics Library for Integrated Tools

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
)

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.

Value

A command object.

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()

blit documentation built on April 12, 2025, 1:16 a.m.