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. Note on base quality score options If the quality score of read bases has been modified in a previous data processing step such as GATK Base Recalibration and an OQ tag is available, this tool can be set to use the OQ value instead of the primary quality value for the evaluation. Note that the default behaviour of this program changed as of November 6th 2015 to no longer include secondary and supplemental alignments in the computation.
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