SAMTOOLS VIEW¶
Convert or filter SAM/BAM.
Software dependencies¶
- samtools ==1.6
Example¶
This wrapper can be used in the following way:
rule samtools_view:
input:
"{sample}.sam"
output:
"{sample}.bam"
params:
"-b" # optional params string
wrapper:
"0.26.1/bio/samtools/view"
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 view {snakemake.params} {snakemake.input[0]} > {snakemake.output[0]}")