# How to output both gVCF and VCF in a single DRAGEN run?

A genomic VCF (**gVCF**) file contains **information on variants and positions determined to be homozygous** to the reference genome. For homozygous regions, the gVCF file includes statistics that indicate how well reads support the absence of variants or alternative alleles. The gVCF file includes an artificial **\<NON\_REF>** allele. Reads that do not support the reference or any variants are assigned the \<NON\_REF> allele.

Including the **'--vc-emit-ref-confidence GVCF'** flag results in a gVCF file being output instead of a VCF file. By default, **contiguous** runs of homozygous reference calls with similar scores are collapsed into blocks (**hom-ref blocks**). Hom-ref blocks save disk space and processing time of downstream analysis tools. To output an unbanded output, users must set --vc-emit-ref-confidence to **BP\_RESOLUTION**.

If a user would like to output a **VCF file** in **addition to a gVCF file**, include the '**--vc-enable-vcf-output true**' flag **in addition to the --vc-emit-ref-confidence** flag. This is the **recommended** way to output a VCF file in runs that output a gVCF. It is **not recommended** to run **DRAGEN Joint Analysis** on the gVCF from a single sample to output a VCF.

More information about the gVCF format can be found in the [user guide](https://support-docs.illumina.com/SW/DRAGEN_v40/Content/SW/DRAGEN/SMVgVCFOutput.htm).

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