PICARD COLLECTTARGETEDPCRMETRICS

Collect metric information for target pcr metrics runs, with picard tools.

Example

This wrapper can be used in the following way:

rule CollectTargetedPcrMetrics:
    input:
        bam="mapped/{sample}.bam",
        amplicon_intervals="amplicon.list",
        target_intervals="target.list"
    output:
        "stats/{sample}.pcr.txt"
    log:
        "logs/picard/collecttargetedpcrmetrics/{sample}.log"
    params:
        extra=""
    # optional specification of memory usage of the JVM that snakemake will respect with global
    # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
    # and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
    # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
    resources:
        mem_mb=1024
    wrapper:
        "0.73.0/bio/picard/collecttargetedpcrmetrics"

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
• snakemake-wrapper-utils==0.1.3

Authors

• Patrik Smeds

Code

__author__ = "Patrik Smeds"
__copyright__ = "Copyright 2019, Patrik Smeds"
__email__ = "patrik.smeds@mail.com"
__license__ = "MIT"


from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts


log = snakemake.log_fmt_shell()

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

shell(
    "picard CollectTargetedPcrMetrics "
    "{java_opts} {extra} "
    "INPUT={snakemake.input.bam} "
    "OUTPUT={snakemake.output[0]} "
    "AMPLICON_INTERVALS={snakemake.input.amplicon_intervals} "
    "TARGET_INTERVALS={snakemake.input.target_intervals} "
    "{log}"
)