Targeted Calling of Internal Tandem Duplications

For the targeted analysis of internal tandem duplications (ITDs), you can increase the sensitivity of the SV caller by allowing overlapping read pairs to be considered as SV evidence using the --sv-use-overlap-pair-evidence true command-line option. If not set, the command is automatically enabled if the fraction of overlapping read pairs is less than 20%.

You can use the --sv-somatic-ins-tandup-hotspot-regions-bed ${BEDFILE} option to specify ITD hotspot regions to increase sensitivity for calling ITDs in somatic variant analysis. By default, DRAGEN SV automatically selects a reference-specific hotspots BED file from /opt/edico/config/sv_somatic_ins_tandup_hotspot_*.bed. The file includes FLT3, ARHGEF7, and KMT2A. To disable this feature, enter --sv-enable-somatic-ins-tandup-hotspot-regions false.