### CollectGcBiasMetrics

Usage: program [options...]

Option | Description
--- | ---
REFERENCE_SEQUENCE=File | The reference sequence fasta file. Required.
INPUT=File | The BAM or SAM file containing aligned reads. Required.
OUTPUT=File | The text file to write the metrics table to. Required.
CHART_OUTPUT=File | The PDF file to render the chart to. Required.
SUMMARY_OUTPUT=File | The text file to write summary metrics to. Default value: null.
WINDOW_SIZE=Integer | The size of windows on the genome that are used to bin reads. Default value: 100. This option can be set to 'null' to clear the default value.
MINIMUM_GENOME_FRACTION=Double | For summary metrics, exclude GC windows that include less than this fraction of the genome. Default value: 1.0E-5. This option can be set to 'null' to clear the default value.