Metrics Output

The Metrics Output File ( MetricsOutput.tsv ) is a final combined metrics report that provides sample status, key analysis metrics, and metadata in a tab-separated values (TSV) file. Sample metrics within the file indicate guideline‑suggested lower specification limits (LSL) and upper specification limits (USL) for each sample in the run.

One Metrics Output File is generated for the entire run. An additional file is generated for each sample.

The Metrics Output File contains the following sections for all samples:

Section	Metrics	Interpretation Details
Header	Output date, time and pipeline version	-
Run QC Metrics	Percentage of reads meeting quality scores (PCT_PF_READS, PCT_Q30_R1 (%), PCT_Q30_R2 (%))	Run QC page
Analysis Status	Completion confirmation, failed and not executed steps	-
DNA Library QC Metrics	Contamination score (CONTAMINATION_SCORE)	Contamination page
DNA Library QC Metrics for Small Variant Calling and TMB	Median exon coverage (MEDIAN_EXON_COVERAGE (count)), percent of exons with 1000X coverage (PCT_EXON_1000X (%))	Sample QC page
DNA Library QC Metrics for MSI and Fusions	Median exon coverage (MEDIAN_EXON_COVERAGE (count))	Sample QC page
DNA Library QC Metrics for CNV Calling	The median of absolute deviations normalized by gene fold change (GENE_SCALED_MAD (count)), the median raw bin count per CNV target.(MEDIAN_BIN_COUNT_CNV_TARGET (count))	Sample QC page
DNA Expanded Metrics	Total reads, mean family size, chimeric reads, and others	DNA Expanded Metrics
Notes	Comments	-