BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

Usage

bcftools(subcmd = NULL, ..., bcftools = NULL)

Arguments

subcmd

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

...

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

bcftools

A string of path to bcftools command.

Value

A command object.

See also

• https://samtools.github.io/bcftools/

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