Metrics
This table summarizes the values that are specific to this metric.
| Metric | Summary |
|---|---|
| ACCUMULATION_LEVEL | |
| READS_USED | This option is used to mark including or excluding duplicates. |
| WINDOW_SIZE | The window size on the genome used to calculate the GC of the sequence. |
| TOTAL_CLUSTERS | The total number of clusters that were seen in the gc bias calculation. |
| ALIGNED_READS | The total number of aligned reads used to compute the gc bias metrics. |
| AT_DROPOUT | Illumina-style AT dropout metric. Calculated by taking each GC bin independently and calculating (%ref_at_gc - %reads_at_gc) and summing all positive values for GC=[0..50]. |
| GC_DROPOUT | Illumina-style GC dropout metric. Calculated by taking each GC bin independently and calculating (%ref_at_gc - %reads_at_gc) and summing all positive values for GC=[50..100]. |
| GC_NC_0_19 | Normalized coverage over quintile of GC content ranging from 0 - 19. |
| GC_NC_20_39 | Normalized coverage over each quintile of GC content ranging from 20 - 39. |
| GC_NC_40_59 | Normalized coverage over each quintile of GC content ranging from 40 - 59. |
| GC_NC_60_79 | Normalized coverage over each quintile of GC content ranging from 60 - 79. |
| GC_NC_80_100 | Normalized coverage over each quintile of GC content ranging from 80 - 100. |
See also General Documentation | Tool Docs Index Tool Documentation Index | Support Forum
GATK version 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.