Output Files

The DRAGEN Host Software generates many intermediate files. *.seg.called.merged is the final call file that contains the amplification and deletion events.

In addition to the segment file, DRAGEN emits the calls in the standard VCF format. By default, the VCF file includes only copy number gain and loss events. For copy neutral segments, refer to the *.seg.called.merged file. To include copy neutral (REF) calls in the output VCF, set --cnv-enable-ref-calls to true.

For more information on the *.seg.called.merged file, and how to use the output files to aid in debug and analysis, see Signal Flow Analysis.