Sambamba

Sambamba

Fast and efficient BAM file processing tool written in D

Citation

Citation: 10.1093/bioinformatics/btv098

Environment

This tool uses the following conda environment:

Channels: - conda-forge - bioconda

Dependencies: - sambamba

Installation

This tool will be automatically installed when first used:

library(ShennongTools)

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

Available Commands

view

Filter and convert BAM/SAM files

Basic Usage:

result <- sn_run("sambamba", "view",
  # Add your parameters here
)

sort

Sort BAM files by coordinate

Basic Usage:

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

index

Create BAM index

Basic Usage:

result <- sn_run("sambamba", "index",
  # Add your parameters here
)

markdup

Mark duplicate reads

Basic Usage:

result <- sn_run("sambamba", "markdup",
  # Add your parameters here
)

flagstat

Print alignment statistics (similar to samtools flagstat)

Basic Usage:

result <- sn_run("sambamba", "flagstat",
  # Add your parameters here
)

Examples

View Example

library(ShennongTools)

result <- sn_run("sambamba", "view",
  input = "input_file.txt",
  output = "output_file.txt",
  threads = 4,
  format = "bam"
)

# 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("sambamba", "sort",
  input = "input_file.txt",
  output = "output_file.txt",
  threads = 4
)

# 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")
}

Index Example

library(ShennongTools)

result <- sn_run("sambamba", "index",
  input = "input_file.txt",
  bai = "example_file",
  threads = 2
)

# 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")
}

Markdup Example

library(ShennongTools)

result <- sn_run("sambamba", "markdup",
  input = "input_file.txt",
  output = "output_file.txt",
  threads = 4
)

# 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")
}

Flagstat Example

library(ShennongTools)

result <- sn_run("sambamba", "flagstat",
  input = "input_file.txt",
  stats = "results.txt",
  threads = 2
)

# 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

view Parameters

Inputs:

Parameter	Type	Required	Description
input	bam, sam, cram	Yes	Input alignment file

Outputs:

Parameter	Type	Required	Description
output	bam, sam	Yes	Output file after filtering or format conversion

Parameters:

Parameter	Type	Default	Description
format	string	“bam”	Output format (bam or sam)
region	string	“”	Region string to extract (e.g., chr1:1000-2000)
threads	integer	4	Number of threads
filter	string	“”	Filtering expression for reads
extras	string	“”	Extra parameters

sort Parameters

Inputs:

Parameter	Type	Required	Description
input	bam	Yes	Input BAM file to sort

Outputs:

Parameter	Type	Required	Description
output	bam	Yes	Sorted BAM file

Parameters:

Parameter	Type	Default	Description
threads	integer	4	Number of threads
memory	string	“4G”	Amount of memory to use per thread
extras	string	“”	Additional parameters

index Parameters

Inputs:

Parameter	Type	Required	Description
input	bam	Yes	BAM file to index

Outputs:

Parameter	Type	Required	Description
bai	bai	Yes	Output index file

Parameters:

Parameter	Type	Default	Description
threads	integer	2	Number of threads
extras	string	“”	Extra options

markdup Parameters

Inputs:

Parameter	Type	Required	Description
input	bam	Yes	Input sorted BAM file

Outputs:

Parameter	Type	Required	Description
output	bam	Yes	Output BAM file with duplicates marked

Parameters:

Parameter	Type	Default	Description
remove_dups	boolean	FALSE	Remove duplicates instead of just marking them
threads	integer	4	Number of threads
extras	string	“”	Additional parameters

flagstat Parameters

Inputs:

Parameter	Type	Required	Description
input	bam	Yes	BAM file to analyze

Outputs:

Parameter	Type	Required	Description
stats	txt	Yes	Output file with alignment statistics

Parameters:

Parameter	Type	Default	Description
threads	integer	2	Number of threads
extras	string	“”	Extra options