SAMTOOLS MERGE

Merge two bam files with samtools. For more information see SAMtools documentation.

URL:

Example

This wrapper can be used in the following way:

rule samtools_merge:
    input:
        ["mapped/A.bam", "mapped/B.bam"]
    output:
        "merged.bam"
    params:
        "" # optional additional parameters as string
    threads:  # Samtools takes additional threads through its option -@
        8     # This value - 1 will be sent to -@
    wrapper:
        "v1.1.0/bio/samtools/merge"

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:

  • list of bam files to merge

Output:

  • merged bam file

Notes

  • Samtools -@/–threads takes one integer as input. This is the number of additional threads and not raw threads.

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