Samtools

Samtools

Utilities for manipulating alignments in the SAM, BAM, and CRAM formats

Citation

Citation: 10.1093/bioinformatics/btp352

Environment

This tool uses the following conda environment:

Channels: - conda-forge - bioconda

Dependencies: - samtools

Installation

This tool will be automatically installed when first used:

library(ShennongTools)

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

Available Commands

view

View and convert SAM/BAM/CRAM files

Basic Usage:

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

index

Create index for BAM/CRAM file

Basic Usage:

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

sort

Sort alignments by leftmost coordinates or by read name

Basic Usage:

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

faidx

Create index for FASTA file

Basic Usage:

result <- sn_run("samtools", "faidx",
  # Add your parameters here
)

fastq

Convert BAM to FASTQ format

Basic Usage:

result <- sn_run("samtools", "fastq",
  # Add your parameters here
)

Examples

View Example

library(ShennongTools)

result <- sn_run("samtools", "view",
  input = "input_file.txt",
  output = "output_file.txt",
  threads = 1,
  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")
}

Index Example

library(ShennongTools)

result <- sn_run("samtools", "index",
  input = "input_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")
}

Sort Example

library(ShennongTools)

result <- sn_run("samtools", "sort",
  input = "input_file.txt",
  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")
}

Faidx Example

library(ShennongTools)

result <- sn_run("samtools", "faidx",
  fasta = "sequences.fasta"
)

# 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")
}

Fastq Example

library(ShennongTools)

result <- sn_run("samtools", "fastq",
  input = "input_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")
}

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, cram	Yes	Output alignment file

Parameters:

Parameter	Type	Default	Description
format	string	“BAM”	Output format (BAM, SAM, CRAM)
threads	integer	1	Number of threads

index Parameters

Inputs:

Parameter	Type	Required	Description
input	bam, cram	Yes	Input file to be indexed

Outputs:

Parameter	Type	Required	Description
index_file	bai, crai	No	Output index file (auto-generated if not specified)

Parameters:

Parameter	Type	Default	Description
threads	integer	1	Number of threads

sort Parameters

Inputs:

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

Outputs:

Parameter	Type	Required	Description
output	bam	Yes	Sorted output file

Parameters:

Parameter	Type	Default	Description
sort_by_name	boolean	FALSE	Sort by read name instead of coordinate
threads	integer	1	Number of threads

faidx Parameters

Inputs:

Parameter	Type	Required	Description
fasta	fasta	Yes	Input FASTA file

Outputs:

Parameter	Type	Required	Description
index	fai	No	FASTA index file (.fai, auto-generated)

fastq Parameters

Inputs:

Parameter	Type	Required	Description
input	bam	Yes	Input BAM file

Outputs:

Parameter	Type	Required	Description
output1	fastq	No	Output FASTQ file for read1 (single-end or paired-end)
output2	fastq	No	Output FASTQ file for read2 (paired-end only)

Parameters:

Parameter	Type	Default	Description
threads	integer	1	Number of threads