dbSNP Annotation

In Germline, Tumor-Normal somatic, or Tumor-Only somatic modes, DRAGEN can look up variant calls in a dbSNP database and add annotations for any matches that it finds there. To enable the dbSNP database search, set the --dbsnp option to the full path to the dbSNP database VCF or .vcf.gz file, which must be sorted in reference order.

For each variant call in the output VCF, if the call matches a database entry for CHROM, POS, REF, and at least one ALT, then the rsID for the matching database entry is copied to the ID column for that call in the output VCF. In addition, DRAGEN adds a DB annotation to the INFO field for calls that are found in the database.

DRAGEN matches variant calls based on the name of the reference sequence/contig, but there is no additional way to assert that the reference used for constructing the dbSNP is the same as the reference used for alignment and variant calling. Make sure that the contigs in the selected annotation database match those in the alignment/variant calling reference.