Key Output Files and Metrics

Navigate to the completed analysis run to review the results.

Results files per sample can be found within the analysis.

Key Output Files

To learn more about key 5-Base specific output files, reference the DRAGEN documentation: https://help.dragen.illumina.com/product-guide/dragen-v4.4/dragen-methylation-pipeline/dragen-5base-pipeline#methylation-calling-outputs

To learn more about non-5-Base specific output files, reference the DRAGEN DNA Pipeline documentation: https://help.dragen.illumina.com/product-guide/dragen-v4.4/dragen-dna-pipeline

CX Report

The *CX_report file will be generated for all analyses. It will have the following format:

• Each line = 1 cytosine in reference genome (with non-zero coverage)​

• # reads can be dedup’d or not, depending on analysis settings (we use dedupping)​

• mC=methylated, C=unmethylated support​

• Overall methylation level = mC_reads / (mC_reads + C_reads)​

• Overall coverage (STRANDED) = mC_reads + C_reads

See the below pages for more information about the key metrics and output files for each of the different analysis types:

• DRAGEN Germline with CNV Variant Calling

• DRAGEN Germline with Small Variant Calling

• DRAGEN Germline with No Variant Calling (Methylation Only)

• DRAGEN Somatic Tumor Only

• DRAGEN Enrichment