SAMTOOLS INDEX

https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/samtools/index?label=version%20update%20pull%20requests

Index bam file with samtools.

Example

This wrapper can be used in the following way:

rule samtools_index:
    input:
        "mapped/{sample}.sorted.bam",
    output:
        "mapped/{sample}.sorted.bam.bai",
    log:
        "logs/samtools_index/{sample}.log",
    params:
        extra="",  # optional params string
    threads: 4  # This value - 1 will be sent to -@
    wrapper:
        "v3.10.2/bio/samtools/index"

Note that input, output and log file paths can be chosen freely.

When running with

snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.

Notes

Software dependencies

  • samtools=1.20

Input/Output

Input:

  • bam file

Output:

  • bam file index (.bai)

Authors

  • Johannes Köster

  • Filipe G. Vieira

Code

__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"


from snakemake.shell import shell

extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)

# Samtools takes additional threads through its option -@
# One thread for samtools merge
# Other threads are *additional* threads passed to the '-@' argument
threads = "" if snakemake.threads <= 1 else " -@ {} ".format(snakemake.threads - 1)

shell(
    "samtools index {threads} {extra} {snakemake.input[0]} {snakemake.output[0]} {log}"
)