diff --git a/src/main/java/picard/analysis/directed/HsMetrics.java b/src/main/java/picard/analysis/directed/HsMetrics.java index 47ec8ad9fe..92e91a985b 100644 --- a/src/main/java/picard/analysis/directed/HsMetrics.java +++ b/src/main/java/picard/analysis/directed/HsMetrics.java @@ -38,8 +38,8 @@ *
  • Metrics that are intended for evaluating the performance of the wet-lab assay that generated the data. * This group includes metrics like the number of bases mapping on/off/near baits, %selected, fold 80 base * penalty, hs library size and the hs penalty metrics. These metrics are calculated prior to some of the - * filters are applied (e.g. low mapping quality reads, low base quality bases and bases overlapping in the middle - * of paired-end reads are all counted). + * filters are applied (e.g. duplicate reads, low mapping quality reads, low base quality bases and bases + * overlapping in the middle of paired-end reads are all counted). *
  • *
  • Metrics for assessing target coverage as a proxy for how well the data is likely to perform in downstream * applications like variant calling. This group includes metrics like mean target coverage, the percentage of bases @@ -82,10 +82,11 @@ public class HsMetrics extends PanelMetricsBase { /** The mean coverage of all baits in the experiment. */ public double MEAN_BAIT_COVERAGE; - /** The number of aligned, de-duped, on-bait bases out of the PF bases available. */ + /** The fraction of aligned, on-bait bases out of the PF bases available. + * (NOTE: This uses duplicate reads for both numerator and denominator) */ public double PCT_USABLE_BASES_ON_BAIT; - /** The number of aligned, de-duped, on-target bases out of all of the PF bases available. */ + /** The fraction of aligned, de-duped, on-target bases out of all the PF bases available. */ public double PCT_USABLE_BASES_ON_TARGET; /** The fold by which the baited region has been amplified above genomic background. */