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.

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