PICARD COLLECTINSERTSIZEMETRICS

Collect metrics on insert size of paired end reads with picard tools.

Example

This wrapper can be used in the following way:

rule insert_size:
    input:
        "mapped/{sample}.bam"
    output:
        txt="stats/{sample}.isize.txt",
        pdf="stats/{sample}.isize.pdf"
    log:
        "logs/picard/insert_size/{sample}.log"
    params:
        # optional parameters (e.g. relax checks as below)
        "VALIDATION_STRINGENCY=LENIENT "
        "METRIC_ACCUMULATION_LEVEL=null "
        "METRIC_ACCUMULATION_LEVEL=SAMPLE"
    # 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/collectinsertsizemetrics"

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
  • r-base==3.6.2
  • snakemake-wrapper-utils==0.1.3

Input/Output

Input:

  • bam file

Output:

  • txt: textual representation of metrics
  • pdf: insert size histogram

Authors

  • Johannes Köster

Code

__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "johannes.koester@protonmail.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
java_opts = get_java_opts(snakemake)


shell(
    "picard CollectInsertSizeMetrics {java_opts} {extra} "
    "INPUT={snakemake.input} OUTPUT={snakemake.output.txt} "
    "HISTOGRAM_FILE={snakemake.output.pdf} {log}"
)