Bioinformatics QC Reporting Tools

Simple scripts to collate per-sample bioinformatic QC metrics. Supports fgbio, Picard, and CSV metric files.

If you say to yourself, "all I want to do is see some QC metrics for my samples", you've come to the right place.

*** This repository is under active development. Use at your own risk. ***

Building and Running

Python 3.6 or higher is required.

To clone the repository: git clone https://github.com/nh13/bfx-qc-reporter.git.

To install locally: python setup.py install.

The tool-chain can be run with bfx-qc-reporter.

Conda Recipe

See the conda-recipe branch.

Reporting QC Metrics

The collation scripts are located in the scripts folder.

Collating QC metrics

The load-metrics command will collate per-sample metric files into a single JSON file for consumption either by the user or by the create-report command. Additionally, a flattened CSV file will also be created. All sample-specific metric files should live in a single directory, and that each metric file for each sample has the same metric extension. For example, the metric file for Picard's AlignmentSummaryMetrics could be located in <output-dir>/<sample-name>.alignment_summary_metrics.txt. The file extension and metrics to be collated are user-configurable with the --metric-defs option; run bfx-qc-reporter load-metrics --help for more information.

Examples

Specifying the name of each sample individually:

python bfx-qc-reporter load-metrics \
    --output-dir <dir-with-metric-files> \
    --output-prefix <output-path-prefix> \
    --sample-names sample1 sample2 ... sampleN

Specifying the sample names using the output of fgbio's DemuxFastqs:

python bfx-qc-reporter load-metrics \
    --output-dir <dir-with-metric-files> \
    --output-prefix <output-path-prefix> \
    --demux-barcode-metrics <path/to/demux_barcode_metrics.txt>

Creating a Summary Report

The create-report command extracts specific metrics from the load-metrics JSON output and writes a JSON file with only those specific metrics. Additionally, a flattened CSV file will also be created. Run bfx-qc-reporter create-report --help for more information.

Example

Using the default metrics to report:

    python bfx-qc-reporter create-report \
        --input </path/to/metrics.json> \
    	--output-prefix <output-path-prefix>;

Specifying a custom set of metrics to report in report_defs.csv:

    python bfx-qc-reporter create-report \
        --input </path/to/metrics.json> \
        --report-defs report_defs.csv \
    	--output-prefix <output-path-prefix>;

Browsing Metrics in Webpage

The src/html/index.html webpage can be used to load the output of load-metrics to allow interactive browsing of metrics across one or more samples. The page also allows the user to sub-select the metrics to display.

*** This functionality is under active development. ***

Help Wanted

The scripts and webpage were written for my own needs, and quickly, on my own free time. Please feel free to contribute!

Example Metric JSON

{
     
    "Sample-1": {
        "Alignment Summary Metrics": {
            "FIRST_OF_PAIR": {
                "total_reads": 10000,
                "pf_reads": 10000,
                "pct_pf_reads": 1,
                "pf_noise_reads": 0,
                "pf_reads_aligned": 9999
            }
        },
        "Duplication Metrics": {
            "None": {
                "library": 1,
                "unpaired_reads_examined": 0,
                "read_pairs_examined": 10000,
                "secondary_or_supplementary_rds": 0,
                "unmapped_reads": 0,
                "unpaired_read_duplicates": 0,
                "read_pair_duplicates": 0,
                "read_pair_optical_duplicates": 0,
                "percent_duplication": 0,
                "estimated_library_size": ""
            }
        }
    },
    "Sample-2": {
        "Alignment Summary Metrics": {
            "FIRST_OF_PAIR": {
                "total_reads": 10000,
                "pf_reads": 10000,
                "pct_pf_reads": 1,
                "pf_noise_reads": 0,
                "pf_reads_aligned": 9999
            }
        },
        "Duplication Metrics": {
            "None": {
                "library": 1,
                "unpaired_reads_examined": 0,
                "read_pairs_examined": 10000,
                "secondary_or_supplementary_rds": 0,
                "unmapped_reads": 0,
                "unpaired_read_duplicates": 0,
                "read_pair_duplicates": 0,
                "read_pair_optical_duplicates": 0,
                "percent_duplication": 0,
                "estimated_library_size": ""
            }
        }
    }        
}

nh13 / bfx-qc-reporter