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:

An example can be found here

Supported Metrics

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.