PICARD MARKDUPLICATES

Mark PCR and optical duplicates with picard tools.

Software dependencies

• picard ==2.22.1

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:
        "0.67.0/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

log = snakemake.log_fmt_shell(stdout=True, stderr=True)

memory = ""
if "mem_mb" in snakemake.resources.keys():
    memory = "-Xmx{}M".format(str(snakemake.resources["mem_mb"]))

shell(
    "picard MarkDuplicates "  # Tool and its subcommand
    "{memory} "  # Automatic Xmx java option
    "{snakemake.params} "  # User defined parmeters
    "INPUT={snakemake.input} "  # Input file
    "OUTPUT={snakemake.output.bam} "  # Output bam
    "METRICS_FILE={snakemake.output.metrics} "  # Output metrics
    "{log}"  # Logging
)