PICARD MARKDUPLICATES

Mark PCR and optical duplicates with picard tools.

Software dependencies

  • picard ==2.9.2

Example

This wrapper can be used in the following way:

rule mark_duplicates:
    input:
        "mapped/{sample}.bam"
    output:
        bam="dedup/{sample}.bam",
        metrics="dedup/{sample}.metrics.txt"
    log:
        "logs/picard/dedup/{sample}.log"
    params:
        "REMOVE_DUPLICATES=true"
    wrapper:
        "0.18.0/bio/picard/markduplicates"

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("picard MarkDuplicates {snakemake.params} INPUT={snakemake.input} "
      "OUTPUT={snakemake.output.bam} METRICS_FILE={snakemake.output.metrics} "
      "&> {snakemake.log}")