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:
        "0.30.0/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]}")