Collect metrics regarding GC bias. This tool collects information about the relative proportions of guanine (G) and cytosine (C) nucleotides in a sample. Regions of high and low G + C content have been shown to interfere with mapping/aligning, ultimately leading to fragmented genome assemblies and poor coverage in a phenomenon known as 'GC bias'. Detailed information on the effects of GC bias on the collection and analysis of sequencing data can be found at DOI: 10.1371/journal.pone.0062856/.
java -jar picard.jar CollectGcBiasMetrics I=input.bam O=gc_bias_metrics.txt CHART=gc_bias_metrics.pdf S=summary_metrics.txt R=reference_sequence.fasta
CHART_OUTPUT (File) The PDF file to render the chart to. Required.
SUMMARY_OUTPUT (File) The text file to write summary metrics to. Required.
SCAN_WINDOW_SIZE (Integer) The size of the scanning windows on the reference 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.
IS_BISULFITE_SEQUENCED (Boolean) Whether the SAM or BAM file consists of bisulfite sequenced reads. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
METRIC_ACCUMULATION_LEVEL (MetricAccumulationLevel) The level(s) at which to accumulate metrics. Default value: [ALL_READS]. This option can be set to 'null' to clear the default value. Possible values: {ALL_READS, SAMPLE, LIBRARY, READ_GROUP} This option may be specified 0 or more times. This option can be set to 'null' to clear the default list.
ALSO_IGNORE_DUPLICATES (Boolean) Use to get additional results without duplicates. This option allows to gain two plots per level at the same time: one is the usual one and the other excludes duplicates. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
INPUT (File) Input SAM or BAM file. Required.
OUTPUT (File) File to write the output to. Required.
ASSUME_SORTED (Boolean) If true (default), then the sort order in the header file will be ignored. Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}
STOP_AFTER (Long) Stop after processing N reads, mainly for debugging. Default value: 0. This option can be set to 'null' to clear the default value.