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"
)
resources:
# This parameter (default 3 GB) can be used to limit the total resources a pipeline is allowed to use, see:
# https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#resources
mem_gb=3
log:
"logs/picard/multiple_metrics/{sample}.log"
params:
# optional parameters
"VALIDATION_STRINGENCY=LENIENT "
"METRIC_ACCUMULATION_LEVEL=null "
"METRIC_ACCUMULATION_LEVEL=SAMPLE "
"REF_FLAT=ref_flat.txt " # is required if RnaSeqMetrics are used
wrapper:
"0.80.1/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==2.23.0
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
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
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
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
shell(
"(picard CollectMultipleMetrics "
"I={snakemake.input.bam} "
"O={out} "
"R={snakemake.input.ref} "
"{extra} {programs} {java_opts}) {log}"
)