Metrics
Category Metrics
Overview
Metrics that are calculated during the PathSeq filterThis table summarizes the values that are specific to this metric.
| Metric | Summary |
|---|---|
| PRIMARY_READS | Number of input reads that are not secondary or supplementary alignments |
| READS_AFTER_PREALIGNED_HOST_FILTER | The number of reads after filtering prealigned reads |
| READS_AFTER_QUALITY_AND_COMPLEXITY_FILTER | The number of reads after low-quality and low-complexity filtering |
| READS_AFTER_HOST_FILTER | The number of reads after host read filtering |
| READS_AFTER_DEDUPLICATION | The number of reads after deduplication |
| FINAL_PAIRED_READS | The number of non-host reads that have mates |
| FINAL_UNPAIRED_READS | The number of non-host unpaired reads |
| FINAL_TOTAL_READS | The number of non-host reads in total |
| LOW_QUALITY_OR_LOW_COMPLEXITY_READS_FILTERED | The number of reads filtered because they were low-quality or low-complexity |
| HOST_READS_FILTERED | The number of subtracted reads identified as host |
| DUPLICATE_READS_FILTERED | The number of filtered duplicate reads |
GATK version 4.6.0.0 built at Sat, 29 Jun 2024 20:47:29 -0400.
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