Chart the nucleotide distribution per cycle in a SAM or BAM fileThis tool produces a chart of the nucleotide distribution per cycle in a SAM or BAM file in order to enable assessment of systematic errors at specific positions in the reads.
java -jar picard.jar CollectBaseDistributionByCycle CHART=collect_base_dist_by_cycle.pdf I=input.bam O=output.txt
CHART_OUTPUT (File) A file (with .pdf extension) to write the chart to. Required.
ALIGNED_READS_ONLY (Boolean) If set to true, calculate the base distribution 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 the base distribution over PF reads only (Illumina specific). PF reads are reads that passed the internal quality filters applied by Illumina sequencers. 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.