Bedtools

A powerful toolset for genome arithmetic.

Citation

Citation: 10.1093/bioinformatics/btq033

Environment

This tool uses the following conda environment:

Channels: - conda-forge - bioconda

Dependencies: - bedtools

Installation

This tool will be automatically installed when first used:

library(ShennongTools)

# Tool will be installed automatically on first use
result <- sn_run("bedtools", "intersect", ...)

Available Commands

intersect

Intersect two sets of genomic features.

Basic Usage:

result <- sn_run("bedtools", "intersect",
  # Add your parameters here
)

merge

Merge overlapping BED intervals.

Basic Usage:

result <- sn_run("bedtools", "merge",
  # Add your parameters here
)

sort

Sort a BED file by chromosomal coordinates.

Basic Usage:

result <- sn_run("bedtools", "sort",
  # Add your parameters here
)

genomecov

Generate genome-wide coverage reports.

Basic Usage:

result <- sn_run("bedtools", "genomecov",
  # Add your parameters here
)

Examples

Intersect Example

library(ShennongTools)

result <- sn_run("bedtools", "intersect",
  a = "regions.bed",
  b = "regions.bed",
  output = "output_file.txt",
  threads = 1
)

# Check if successful
if (sn_is_toolcall_success(result)) {
  cat("Command completed successfully!\n")
} else {
  cat("Command failed. Check logs:\n")
  cat(readLines(result@log_file), sep = "\n")
}

Merge Example

library(ShennongTools)

result <- sn_run("bedtools", "merge",
  input = "input_file.txt",
  output = "output_file.txt"
)

# Check if successful
if (sn_is_toolcall_success(result)) {
  cat("Command completed successfully!\n")
} else {
  cat("Command failed. Check logs:\n")
  cat(readLines(result@log_file), sep = "\n")
}

Sort Example

library(ShennongTools)

result <- sn_run("bedtools", "sort",
  input = "input_file.txt",
  output = "output_file.txt"
)

# Check if successful
if (sn_is_toolcall_success(result)) {
  cat("Command completed successfully!\n")
} else {
  cat("Command failed. Check logs:\n")
  cat(readLines(result@log_file), sep = "\n")
}

Genomecov Example

library(ShennongTools)

result <- sn_run("bedtools", "genomecov",
  input = "input_file.txt",
  output = "output_file.txt"
)

# Check if successful
if (sn_is_toolcall_success(result)) {
  cat("Command completed successfully!\n")
} else {
  cat("Command failed. Check logs:\n")
  cat(readLines(result@log_file), sep = "\n")
}

Parameters Reference

intersect Parameters

Inputs:

Parameter	Type	Required	Description
`a`	bed	Yes	First input BED file
`b`	bed	Yes	Second input BED file

Outputs:

Parameter	Type	Required	Description
`output`	bed	Yes	Output BED file with intersections

Parameters:

Parameter	Type	Default	Description
`threads`	integer	1	Number of threads to use (not applicable, but included for consistency)
`extras`	string	“”	Extra parameters to pass to bedtools

merge Parameters

Inputs:

Parameter	Type	Required	Description
`input`	bed	Yes	Input BED file

Outputs:

Parameter	Type	Required	Description
`output`	bed	Yes	Output merged BED file

Parameters:

Parameter	Type	Default	Description
`extras`	string	“”	Extra parameters to pass to bedtools

sort Parameters

Inputs:

Parameter	Type	Required	Description
`input`	bed	Yes	Input BED file

Outputs:

Parameter	Type	Required	Description
`output`	bed	Yes	Sorted BED file

Parameters:

Parameter	Type	Default	Description
`faidx`	string	“”	Optional genome file for sorting order
`extras`	string	“”	Extra parameters

genomecov Parameters

Inputs:

Parameter	Type	Required	Description
`input`	bed	Yes	Input BED file

Outputs:

Parameter	Type	Required	Description
`output`	bed	Yes	Output coverage file

Parameters:

Parameter	Type	Default	Description
`genome`	string	“”	Path to genome file with chromosome sizes
`bga`	boolean	FALSE	Report coverage as BedGraph (BGA)
`extras`	string	“”	Extra parameters