GcBiasSummaryMetrics – GATK

Metrics

Overview

High level metrics that capture how biased the coverage in a certain lane is. @author Tim Fennell

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.

GATK version 4.6.0.0 built at Sat, 29 Jun 2024 20:47:29 -0400.