Collect mean quality by cycle.This tool generates a data table and chart of mean quality by cycle from a BAM file. It is intended to be used on a single lane or a read group's worth of data, but can be applied to merged BAMs if needed. This metric gives an overall snapshot of sequencing machine performance. For most types of sequencing data, the output is expected to show a slight reduction in overall base quality scores towards the end of each read. Spikes in quality within reads are not expected and may indicate that technical problems occurred during sequencing.
java -jar picard.jar MeanQualityByCycle I=input.bam O=mean_qual_by_cycle.txt CHART=mean_qual_by_cycle.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}
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.