Handling Decoy Contigs

The DRAGEN hash table builder automatically detects the absence of the decoy contigs from the reference and adds the decoy contigs to the FASTA file, prior to building the hash table. The decoys file is found at /opt/edico/liftover/hs_decoys.fa. If the reference is missing the decoy contigs, then the reads that map to the decoy contigs are artificially marked as unmapped in the output BAM because the original reference does not have the decoy contig. This results in an artificially lower mapping rate. However, the removal of false positive caused by decoy reads results in improved accuracy of variant calling.

Illumina recommends using this feature by default. However, you can set the --ht-suppress-decoys option to true to suppress adding these decoys to the hash table.