java -jar picard.jar QualityScoreDistribution I=input.bam O=qual_score_dist.txt CHART=qual_score_dist.pdf
CHART_OUTPUT (File) A file (with .pdf extension) to write the chart to. Required.
ALIGNED_READS_ONLY (Boolean) If set to true calculate mean quality over aligned reads only. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
PF_READS_ONLY (Boolean) If set to true calculate mean quality over PF reads only. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
INCLUDE_NO_CALLS (Boolean) If set to true, include quality for no-call bases in the distribution. 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.