Biobambam markduplicates

Tools for early stage alignment file processing

Software dependencies

• biobambam >=2.0.87

Example

rule biobambam_markduplicates:
  input:
    "mapped/{sample}.bam" # Path to a bam file.
  output:
    "mapped/{sample}.dedup.bam" # Path the deduplicated bam file.
  params:
    options = "" # Additional command line options.
  wrapper:
    "biobambam/markduplicates"

Usage

Run snakemake with

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

to automatically download the wrapper biobambam/markduplicates 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

• Jens Preussner