DNA Output

Refer to DNA Analysis Methods for more information.

Small Variant Genome VCF

File name: {SAMPLE_ID}_hard-filtered.gvcf.gz

The small variant genome VCF file includes the variant call status for all targeted intervals, left-padded by 25 bp.

The Epidermal Growth Factor Receptor (EGFR) complex variant VCF includes phased EGFR variants. The FILTER column in the genome VCF determines the variant status. Refer to the following table for more information.

ALT	FILTER	Note
.	PASS	WT.
., A, C, G, etc1	low_depth²	Reference or filtered variant candidate with depth < 1000.
A, C, G, etc1	PASS	PASS variants.
A, C, G, etc1	weak_evidence	Filtered variant candidate with the following conditions:
		Filtered variant candidate with low SQ score (< 2).
A, C, G, etc1	excluded_regions³	Position with high background noise. Not available for variant detection.
A, C, G, etc1	systematic_noise	Filtered variant candidate with low AQ score (< 20 for hotspots, < 60 for nonhotspots).
A, C, G, etc1	mapping_quality	Filtered variant candidate with low median mapping quality (< 30).
A, C, G, etc1	read_position	Filtered variant candidate showed bias clustered at fragment ends.
A, C, G, etc1	multiallelic	Filtered if there are two or more ALT alleles at this location.
A, C, G, etc1	low_frac_info_reads	Filtered if the fraction of informative reads is low (< 0.5).

¹ Etc refers to other variant types not mentioned in the table.

² Reference positions and nonpassing variants with coverage below 1000X directly translate into low_depth. For variant calls, low_depth is not applied when a position has a PASS filter.

³ This is a static list of regions compiled by Illumina. Email Illumina Technical Support for more information.

Small Variant Annotated JSON

File name: {SAMPLE_ID}_DNAVariants_Annotated.json.gz

The small variants annotated file provides variant annotation information for all non-reference positions in the VCF, which includes non-pass variants. The variant consequence definition is available on the Sequence Ontology website.

All pass variant calls are annotated using the Illumina Annotation Engine (IAE), also known as Nirvana, with the following information (using the RefSeq transcript):

• HGNC Gene

  • Transcript

  • Exon

  • Consequence

  • c.HGVS

  • p.HGVS

• COSMIC

TMB Trace

File name: {Sample_ID}.tmb.metrics.csv

The TMB metrics file contains the tumor mutational burden metrics for each DNA sample. The file format uses the following CSV column convention, similar to other metric CSV files.

Column	Description
Filtered Variant Count	Remaining variants after variant and germline filters.
Eligible Region (MB)	The specified custom regions, in megabases, that meet the minimum coverage threshold.
TMB	Filtered variants normalized by the eligible regions.

Sample Analysis Results JSON

File name: {SampleID}_SampleAnalysisResults.json

The sample analysis results file (SARJ) is an aggregated results file created for each sample. The SARJ file is used for the generation of downstream outputs. The file contains passing variants and passing variant annotations.

Copy Number Variants VCF

File name: {Sample_ID}_cnv.vcf

The copy number variants (CNV) file contains calls for DNA libraries of the CNV genes targeted by TruSight Oncology 500 ctDNA v2 and v1 assays. The CNV call indicates fold change results for each gene classified as reference, deletion, or amplification.

The value in the QUAL column of the copy number variants VCF is a Phred transformation of the p-value represented by the following equation:\

The p-value is derived from the t-test between the fold change (FC) of the gene against the rest of the genome. Higher Q-scores indicate higher confidence in the CNV call.

In the VCF notation, <DUP> indicates the detected FC is greater than a predefined amplification cutoff. <DEL> indicates the FC is less than a predefined deletion cutoff for that gene. This cutoff can vary from gene to gene.

Each copy number variant is reported as the fold change on normalized read depth in a testing sample relative to the normalized read depth in diploid genomes. Given tumor purity, the ploidy of a gene in the sample can be inferred from the reported fold change.\

Given tumor purity X%, for a reported fold change Y, the copy number n can be calculated by using the following equation:

For example, in a testing sample of tumor purity at 30%, MET with a fold change of 2.2x indicates that 10 copies of MET DNA are observed.

Copy Number Variants Metrics CSV

Copy number variant metrics are reported on a per sample level.

• Sex Genotyper—The predicted sex of the sample.

• Number of alignment records—The number of alignment records in the sample.

• Bases in reference genome—The number of bases in the reference genome.

• Average alignment coverage over genome—The average alignment coverage across the reference genome.

• Number of filtered records (total)—The number of total filtered records.

• Number of filtered records (duplicates)—The number of duplicated filtered records.

• Number of filtered records (MAPQ)—The number of MAPQ filtered records.

• Number of filtered records (unmapped)—The number of unmapped filtered records.

• Number of target intervals—The number of target intervals in the sample.

• Number of segments—The number of segments in the sample. Applicable only to CNV SLM mode.

• Number of amplifications—The number of amplifications in the sample. Applicable only to CNV SLM mode.

• Number of deletions—The number of deletions in the sample. Applicable only to CNV SLM mode.

• Number of passing amplifications—The number of passing amplifications in the sample. Applicable only to CNV SLM mode.

• Number of passing deletions—The number of passing deletions in the sample. Applicable only to CNV SLM mode.

Small Variant VCF

File name: {SampleID}_hard-filtered.vcf

The small variant file contains both phased variants and all other small variants. The header sections from both the phased variant (complex) VCF and the small variant VCF are included in this merged VCF. Variants that are found for both phased variants and small variants are only displayed as phased variants.

Fusions CSV

File name: {Sample_ID}_Fusions.csv

The fusions file contains all candidate fusions identified by the analysis pipeline.

The fusion columns are described in the following table. If you use Microsoft Excel to view this file, genes that are convertible to dates (for example, MARCH1) automatically convert to dd‑mm format (1-Mar).

Fusion Object Field	Description
Sample	Input sample ID.
Name	Fusion name as reported by the DRAGEN fusion caller.
Chr1	The chromosome of the first breakend.
Pos1	The position of the first breakend.
Chr2	The chromosome of the second breakend.
Pos2	The position of the second breakend.
Direction	The direction of how the breakends are joined.
Alt_Depth	The number of read-pairs supporting the fusion call.
Total_Depth	Max number of read-pairs aligned to a fusion breakend.
BP1_Depth	Number of read-pairs aligned to the first breakend.
BP2_Depth	Number of read-pairs aligned to the second breakend.
VAF	Variant allele frequency.
Gene1	Genes that overlap the first breakend.
Gene2	Genes that overlap the second breakend.
Contig	The fusion contig.
Filter	Indicates whether the fusion has passed all of the fusion filters.
Is_Cosmic_GenePair	Indicates whether the gene pair has been reported by COSMIC (True/False).
Fusion Directionality Known	Indicates whether the fusion direction is known, and indicated by the order of the genes (True/False).

The following table lists the meaning of the values in the direction column. The values are in the format used by Samtools.

Direction	VCF Format	Description
L1R2	t[p[	The left of breakend1 is joined with the right of breakend2.
L1rL2	t]p]	The left of breakend1 is joined with the reverse complement of the left of breakend2.
L2R1	]p]t	The left of breakend2 is joined with the right of breakend1.
rR2R1	[p[t	The reverse complement of the right of breakend2 is joined with the right of breakend1.