Sambamba sort

Sort bam file with sambamba

Software dependencies

• sambamba ==0.6.6

Example

rule sambamba_sort:
  input:
    "mapped/{sample}.bam" # A bam file
  output:
    "mapped/{sample}.sorted.bam" # A sorted bam file
  wrapper:
    "sambamba/sort"

Usage

Run snakemake with

snakemake --wrapper-prefix https://github.molgen.mpg.de/raw/loosolab/snakemake-wrappers/master/

to automatically download the wrapper sambamba/sort and include it in the snakefile.

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