SAMTOOLS MERGE¶
Merge two bam files with samtools.
Software dependencies¶
- samtools ==1.6
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:
"0.32.0/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.
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}")