PICARD COLLECTTARGETEDPCRMETRICS

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

Software dependencies

  • picard ==2.22.1

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=""
    wrapper:
        "0.65.0/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.

Authors

  • Patrik Smeds

Code

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


from snakemake.shell import shell


log = snakemake.log_fmt_shell()

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

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