> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/dragen-5-base/additional-information/key-output-files-and-metrics/dragen-germline-with-cnv-variant-calling.md). # DRAGEN Germline with CNV Variant Calling ### Primary Annotation Files * bam​ * cnv.vcf.gz​ * control.CX\_report.txt.gz​ * CX\_report.txt.gz​ * gvcf.gz​ * vcf.gz​ * cnv\_sv.vcf.gz (Note: This file will only appear if \*cnv.metrics.csv has called CNVs and they're passing) ### Primary Metrics Files * cnv\_metrics.csv​ * fastqc\_metrics.csv​ * gvcf\_metrics.csv​ * fragment\_length\_hist.csv​ * lambda\_unmethylated\_control.control.M-bias.txt​ * puc19\_methylated\_control.control.M-bias.txt​ * M-bias.txt​ * mapping\_metrics.csv​ * methyl\_metrics.csv​ * vc\_metrics.csv​ * wgs\_contig\_mean\_cov.csv​ * wgs\_coverage\_metrics.csv​ * wgs\_overall\_mean\_cov.csv ### Mapping / Alignment Metrics The following can be extracted from \*mapping\_metrics.csv files: * Total reads​ * Total bases​ * Mapped reads percentage​ * Paired reads mapped to different chromosomes (MAPQ>=10) percentage​ * Mismatched bases R1 (excl. indels) percentage​ * Mismatched bases R1 (excl. indels) percentage​ * Q30 bases percentage​ * Not properly paired reads (discordant) percentage​ * Percentage of duplicate marked reads​ * Percentage of reads with MAPQ > 40​ * Soft-clipped bases R1​ * Soft-clipped bases R2 ### Coverage Metrics The following can be extracted from \*wgs\_coverage\_metrics.csv files: * Uniformity of coverage, percent of bases with coverage > 0.2 \* mean coverage​ * PCT of genome with coverage \[0x: 1x)​ * Average autosomal coverage over genome ### Methylation Calling Metrics The following can be extracted from \*methyl\_metrics.csv files: * % of Cs methylated in CpG context (tag in csv file: mCpGPer)​ * % of Cs methylated in CHG context (tag in csv file: mCHGPer)​ * % of Cs methylated in CHH context (tag in csv file: mCHHPer)​ * % of Cs methylated in unknown context (tag in csv file: mCunkPer)​ * The same 4 %C methylation metrics will be reported for the lambda and puc19 control genomes ### M-bias Metrics The following can be extracted from \*M-bias.txt files: * Counts of methylated and unmethylated Cs * % methylation and coverage for each position in read1 and read2 for CpG, CHG, and CHH contexts --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation by asking a question. Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters: ``` GET https://help.bioinsight.illumina.com/dragen-5-base/additional-information/key-output-files-and-metrics/dragen-germline-with-cnv-variant-calling.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.