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¶
- The java_opts param allows for additional arguments to be passed to the java compiler, e.g. “-XX:ParallelGCThreads=10” (not for -XmX or -Djava.io.tmpdir, since they are handled automatically).
- The extra param allows for additional program arguments.
- –TMP_DIR is automatically set by resources.tmpdir
- For more information see, https://broadinstitute.github.io/picard/command-line-overview.html#CollectMultipleMetrics
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}"
)