Collect metrics about reads that pass quality thresholds and Illumina-specific filters. This tool evaluates the overall quality of reads within a bam file containing one read group. The output indicates the total numbers of bases within a read group that pass a minimum base quality score threshold and (in the case of Illumina data) pass Illumina quality filters as described in the GATK Dictionary entry.
java -jar picard.jar CollectQualityYieldMetrics I=input.bam O=quality_yield_metrics.txt \
USE_ORIGINAL_QUALITIES (Boolean) If available in the OQ tag, use the original quality scores as inputs instead of the quality scores in the QUAL field. Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}
INCLUDE_SECONDARY_ALIGNMENTS (Boolean) If true, include bases from secondary alignments in metrics. Setting to true may cause double-counting of bases if there are secondary alignments in the input file. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
INCLUDE_SUPPLEMENTAL_ALIGNMENTS (Boolean) If true, include bases from supplemental alignments in metrics. Setting to true may cause double-counting of bases if there are supplemental alignments in the input file. 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.