PICARD MARKDUPLICATESWITHMATECIGAR

Mark PCR and optical duplicates with picard tools, taking into account the CIGAR of the mate. For more information about MarkDuplicatesWithMateCigar see picard documentation.

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"
    resources:
        mem_mb=1024
    wrapper:
        "0.68.0/bio/picard/markduplicateswithmatecigar"

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.

Software dependencies

• picard==2.22.1

Input/Output

Input:

• bam file

Output:

• bam file with marked or removed duplicates

Authors

• Johannes Köster
• Filipe G. Vieira

Code

__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"


from snakemake.shell import shell


extra = snakemake.params.get("extra", "")
java_opts = snakemake.params.get("java_opts", "")

# Getting memory in megabytes, if java opts is not filled with -Xmx parameter
# By doing so, backward compatibility is preserved
if "mem_mb" in snakemake.resources.keys() and not "-Xmx" in java_opts:
    java_opts += " -Xmx{}M".format(snakemake.resources["mem_mb"])

# Getting memory in gigabytes, for user convenience. Please prefer the use
# of mem_mb over mem_gb as advised in documentation.
elif "mem_gb" in snakemake.resources.keys() and not "-Xmx" in java_opts:
    java_opts += " -Xmx{}G".format(snakemake.resources["mem_gb"])

# Getting java temp directory from output files list, if -Djava.io.tmpdir
# is not provided in java parameters. By doing so, backward compatibility is
# not borken.
if "java_temp" in snakemake.output.keys() and not "-Djava.io.tmpdir" in java_opts:
    java_opts += " -Djava.io.tmpdir={}".format(snakemake.output["java_temp"])


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


shell(
    "picard MarkDuplicatesWithMateCigar {java_opts} {extra} INPUT={snakemake.input} "
    "OUTPUT={snakemake.output.bam} METRICS_FILE={snakemake.output.metrics} "
    "{log}"
)