qc-metric-aggregator 0.1.2

Given the output directory of a QC pipeline and a threshold config file, parse out the desired metrics and evalute them against the thresholds.

qc-metric-aggregator

Parse individual metrics out of a directory of QC results for genomic data and output a report containing the desired metrics and the overall PASS/FAIL status of the sample.

Installation

---

pip install qc-metric-aggregator

---

Usage

---

usage: aggregate-qc-metrics [-h]
                            sample_name metrics_dir output_file threshold_file

positional arguments:
  sample_name     The sample name or id for which the QC metrics apply
  metrics_dir     The directory to search for metric files, often a cromwell
                  run directory
  output_file     File path to store the finalized mertrics TSV
  threshold_file  Path to the yml thresholds file to validate against

optional arguments:
  -h, --help      show this help message and exit

Example invocation:

aggregate-qc-metrics HG00096 /opt/qc/results/HG00096/WholeGenomeSingleSampleQc /opt/qc/scores/qc_results.tsv thresholds.yml

---

Output formats

Coming soon...

---

Threshold file

You will need to pass in a YAML file containing pass/fail threshold tests for the metrics you are interested in. The file format consists of a list of objects each containing the following keys:

Key	Value	Comments
metric_name	Name of the metric to check	This can be any supported metric and should be the value returned by name.
operator	Which operation to use to compare the metric value to the PASS/FAIL threshold	<,<=,>,>=, and = are all supported. If you instead specify report the metric will be reported in the final output, but not factored into the PASS/FAIL status.
value	The PASS/FAIL threshold to compare the metric value to	This field is optional if report is specified for the operator.

An example can be found here

---

Supported Metrics

Name	Description	Originating Tool
FREEMIX	Freemix	VerifyBamId2
Q20_BASES	Total bases with Q20 or higher	Picard CollectQualityYieldMetrics
MEAN_COVERAGE	Haploid Coverage	Picard CollectWgsMetrics
PCT_10X	Percent coverage at 10x	Picard CollectWgsMetrics
PCT_20X	Percent coverage at 20x	Picard CollectWgsMetrics
PCT_30X	Percent coverage at 30x	Picard CollectWgsMetrics
PCT_CHIMERAS	Percent chimeras (PAIR)	Picard CollectAlignmentSummaryMetrics
READ1_PF_MISMATCH_RATE	Read 1 base mismatch rate	Picard CollectAlignmentSummaryMetrics
READ2_PF_MISMATCH_RATE	Read 2 base mismatch rate	Picard CollectAlignmentSummaryMetrics
MEDIAN_INSERT_SIZE	Library insert size median	Picard CollectInsertSizeMetrics
MEDIAN_ABSOLUTE_DEVIATION	Library insert size mad	Picard CollectInsertSizeMetrics
PERCENT_DUPLICATION	Percent duplicate marked reads	Picard CollectDuplicateMetrics

---

Adding Additional Metrics

To add support for additional metrics you simply need to subclass Metric and register it in AvailableMetrics

Because many QC metrics are output in TSV format, there is a helper class TSVMetric that you can inherent from in addition to Metric that will make that easier. All of the currently supported metrics use this helper, so you should be able to look to them for examples.