PICARD COLLECTMULTIPLEMETRICS

A picard meta-metrics tool that collects multiple classes of metrics. For usage information about CollectMultipleMetrics, please see picard’s documentation. For more information about picard, also see the source code.

You can select which tool(s) to run by adding the respective extension(s) (see table below) to the requested output of the wrapper invocation (see example Snakemake rule below).

Tool Extension(s) for the output files
CollectAlignmentSummaryMetrics “.alignment_summary_metrics”
CollectInsertSizeMetrics

“.insert_size_metrics”,

“.insert_size_histogram.pdf”

QualityScoreDistribution

“.quality_distribution_metrics”,

“.quality_distribution.pdf”

MeanQualityByCycle

“.quality_by_cycle_metrics”,

“.quality_by_cycle.pdf”

CollectBaseDistributionByCycle

“.base_distribution_by_cycle_metrics”,

“.base_distribution_by_cycle.pdf”

CollectGcBiasMetrics

“.gc_bias.detail_metrics”,

“.gc_bias.summary_metrics”,

“.gc_bias.pdf”

RnaSeqMetrics “.rna_metrics”
CollectSequencingArtifactMetrics

“.bait_bias_detail_metrics”,

“.bait_bias_summary_metrics”,

“.error_summary_metrics”,

“.pre_adapter_detail_metrics”,

“.pre_adapter_summary_metrics”

CollectQualityYieldMetrics “.quality_yield_metrics”

URL:

Example

This wrapper can be used in the following way:

rule collect_multiple_metrics:
    input:
        bam="mapped/{sample}.bam",
        ref="genome.fasta",
    output:
        # Through the output file extensions the different tools for the metrics can be selected
        # so that it is not necessary to specify them under params with the "PROGRAM" option.
        # Usable extensions (and which tools they implicitly call) are listed here:
        #         https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/picard/collectmultiplemetrics.html.
        multiext(
            "stats/{sample}",
            ".alignment_summary_metrics",
            ".insert_size_metrics",
            ".insert_size_histogram.pdf",
            ".quality_distribution_metrics",
            ".quality_distribution.pdf",
            ".quality_by_cycle_metrics",
            ".quality_by_cycle.pdf",
            ".base_distribution_by_cycle_metrics",
            ".base_distribution_by_cycle.pdf",
            ".gc_bias.detail_metrics",
            ".gc_bias.summary_metrics",
            ".gc_bias.pdf",
            ".rna_metrics",
            ".bait_bias_detail_metrics",
            ".bait_bias_summary_metrics",
            ".error_summary_metrics",
            ".pre_adapter_detail_metrics",
            ".pre_adapter_summary_metrics",
            ".quality_yield_metrics",
        ),
    # 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_gb=3,
    log:
        "logs/picard/multiple_metrics/{sample}.log",
    params:
        # optional parameters
        # REF_FLAT is required if RnaSeqMetrics are used
        extra="--VALIDATION_STRINGENCY LENIENT --METRIC_ACCUMULATION_LEVEL null --METRIC_ACCUMULATION_LEVEL SAMPLE --REF_FLAT ref_flat.txt",
    wrapper:
        "v1.1.0/bio/picard/collectmultiplemetrics"

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=2.26
  • snakemake-wrapper-utils==0.1.3

Input/Output

Input:

  • BAM file (.bam)
  • FASTA reference sequence file (.fasta or .fa)

Output:

  • multiple metrics text files (_metrics) AND
  • multiple metrics pdf files (.pdf)
  • the appropriate extensions for the output files must be used depending on the desired tools

Notes

Authors

  • David Laehnemann
  • Antonie Vietor

Code

__author__ = "David Laehnemann, Antonie Vietor"
__copyright__ = "Copyright 2020, David Laehnemann, Antonie Vietor"
__email__ = "antonie.v@gmx.de"
__license__ = "MIT"

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

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

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

exts_to_prog = {
    ".alignment_summary_metrics": "CollectAlignmentSummaryMetrics",
    ".insert_size_metrics": "CollectInsertSizeMetrics",
    ".insert_size_histogram.pdf": "CollectInsertSizeMetrics",
    ".quality_distribution_metrics": "QualityScoreDistribution",
    ".quality_distribution.pdf": "QualityScoreDistribution",
    ".quality_by_cycle_metrics": "MeanQualityByCycle",
    ".quality_by_cycle.pdf": "MeanQualityByCycle",
    ".base_distribution_by_cycle_metrics": "CollectBaseDistributionByCycle",
    ".base_distribution_by_cycle.pdf": "CollectBaseDistributionByCycle",
    ".gc_bias.detail_metrics": "CollectGcBiasMetrics",
    ".gc_bias.summary_metrics": "CollectGcBiasMetrics",
    ".gc_bias.pdf": "CollectGcBiasMetrics",
    ".rna_metrics": "RnaSeqMetrics",
    ".bait_bias_detail_metrics": "CollectSequencingArtifactMetrics",
    ".bait_bias_summary_metrics": "CollectSequencingArtifactMetrics",
    ".error_summary_metrics": "CollectSequencingArtifactMetrics",
    ".pre_adapter_detail_metrics": "CollectSequencingArtifactMetrics",
    ".pre_adapter_summary_metrics": "CollectSequencingArtifactMetrics",
    ".quality_yield_metrics": "CollectQualityYieldMetrics",
}
progs = set()

for file in snakemake.output:
    matched = False
    for ext in exts_to_prog:
        if file.endswith(ext):
            progs.add(exts_to_prog[ext])
            matched = True
    if not matched:
        sys.exit(
            "Unknown type of metrics file requested, for possible metrics files, see https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/picard/collectmultiplemetrics.html"
        )

programs = " --PROGRAM " + " --PROGRAM ".join(progs)

out = str(snakemake.wildcards.sample)  # as default
output_file = str(snakemake.output[0])
for ext in exts_to_prog:
    if output_file.endswith(ext):
        out = output_file[: -len(ext)]
        break

with tempfile.TemporaryDirectory() as tmpdir:
    shell(
        "picard CollectMultipleMetrics"
        " {java_opts} {extra}"
        " --INPUT {snakemake.input.bam}"
        " --TMP_DIR {tmpdir}"
        " --OUTPUT {out}"
        " --REFERENCE_SEQUENCE {snakemake.input.ref}"
        " {programs}"
        " {log}"
    )