SAMTOOLS MERGE

Merge two bam files with samtools.

Software dependencies

  • samtools ==1.5

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: 8
    wrapper:
        "0.19.3/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.

Authors

  • Johannes Köster

Code

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


from snakemake.shell import shell


shell("samtools merge --threads {snakemake.threads} {snakemake.params} "
      "{snakemake.output[0]} {snakemake.input}")