PICARD COLLECTHSMETRICS

Collects hybrid-selection (HS) metrics for a SAM or BAM file using picard.

Example

This wrapper can be used in the following way:

rule picard_collect_hs_metrics:
    input:
        bam="mapped/{sample}.bam",
        reference="genome.fasta",
        # Baits and targets should be given as interval lists. These can
        # be generated from bed files using picard BedToIntervalList.
        bait_intervals="regions.intervals",
        target_intervals="regions.intervals"
    output:
        "stats/hs_metrics/{sample}.txt"
    params:
        # Optional extra arguments. Here we reduce sample size
        # to reduce the runtime in our unit test.
        extra="SAMPLE_SIZE=1000"
    # 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
    log:
        "logs/picard_collect_hs_metrics/{sample}.log"
    wrapper:
        "0.73.0/bio/picard/collecthsmetrics"

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

Input/Output

Input:

• bam file

Output:

• metrics file

Authors

• Julian de Ruiter

Code

"""Snakemake wrapper for picard CollectHSMetrics."""

__author__ = "Julian de Ruiter"
__copyright__ = "Copyright 2017, Julian de Ruiter"
__email__ = "julianderuiter@gmail.com"
__license__ = "MIT"


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


inputs = " ".join("INPUT={}".format(in_) for in_ in snakemake.input)
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
java_opts = get_java_opts(snakemake)

shell(
    "picard CollectHsMetrics"
    " {java_opts} {extra}"
    " INPUT={snakemake.input.bam}"
    " OUTPUT={snakemake.output[0]}"
    " REFERENCE_SEQUENCE={snakemake.input.reference}"
    " BAIT_INTERVALS={snakemake.input.bait_intervals}"
    " TARGET_INTERVALS={snakemake.input.target_intervals}"
    " {log}"
)