SAMTOOLS INDEX

Index bam file with samtools. For more information see SAMtools documentation.

URL:

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:
        "" # optional params string
    threads:  # Samtools takes additional threads through its option -@
        4     # This value - 1 will be sent to -@
    wrapper:
        "v1.1.0/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.

Software dependencies

• samtools==1.10

Input/Output

Input:

• bam file

Output:

• bam file index (.bai)

Authors

• Johannes Köster

Code

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


from snakemake.shell import shell

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} {snakemake.params} {snakemake.input[0]} {snakemake.output[0]} {log}"
)